Help, Index & Glossary for Protein Explorer (PE).
PE's Reference Manual.
(The only GREEN document in PE.)
by Eric Martz. Some entries contributed by Diana Ditmore.

Released April 2001 (~100 terms) and continuously updated. June 2001: ~150 terms; August 2001: ~200 terms; April 2004: ~270 terms; August 2005: ~300 terms.
This document is updated frequently, more often than is the downloadable version of PE. If you can't find something, check on-line at proteinexplorer.org, for the very latest version of this document.

Can't find it? Please email suggestions for new entries in this index/glossary (or for additional information under existing entries) to Eric Martz. My goal is that the term you first think of should be here -- at least as a cross reference to another entry!

If the term you want is not in the alphabetic list below, try your web browser's Edit, Find (in document) to see if it occurs anywhere below.

Protein Explorer (PE) is designed to be, as much as possible, self-explanatory. PE's FrontDoor has a wealth of introductory information. Beginners wishing an introductory overview should start with the flash movies that demonstrate PE, and then proceed to the 1-Hour Tour. When you don't know how to get the result you want, consult the Help, Index & Glossary/PE Reference Manual below -- it is always available within PE by clicking , or through the PE Site Map, or a link on the FrontDoor. Throughout PE, most links to entries here are colored green: this is the only green document in PE. See also the Frequently Asked Questions (FAQ). Finally, the Tutorial provides a truly comprehensive tour.

Here are some Tips & Techniques for using PE effectively. Gale Rhodes (Univ. Southern Maine) has provided an excellent Glossary of Terms from Crystallography, NMR, and Homology Modeling.

Teachers: See the Lesson Plans and Assessment Questions.

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Acknowledgements

Advanced Explorer

Advanced Explorer links to a number of powerful control panels and resources. Some of these require familiarity with the command language. To get to Advanced Explorer, look for the link PE Site Map in the current control panel. You may have to scroll the control panel up or down to find it. There is also a command to PE that will take you to Advanced Explorer: enter the command .x ("x" preceded by a period).

Aliases, command.

Commands may be entered as abbreviations called "aliases". For more information, click the link Aliases below the message box.

Alignments.

The term "Alignment" can refer either to alignments of sequences, or of structures. For sequences, see MSA3D. Instructions are also available for making structural alignments.

Amino acids

The twenty standard amino acids are listed in the top frame of the Sequences and Seq3D displays (available from the PE Site Map), or in QuickViews with DISPLAY Sequences). Sequences are given in one-letter code, but touching any letter shows its three letter code. For convenience, the codes are also listed here. Mnemonic names are shown in quotations, followed by the correctly spelled name in parentheses.

Ala A Alanine Arg R aRginine Asn N asparagiNe Asp D "asparDic" (aspartic) acid Cys C Cysteine

Gln Q "Quetamine" (glutamine) Glu E "gluEtamic" (glutamic) acid Gly G Glycine His H Histidine Ile I Isoleucine

Leu L Leucine Lys K "liKesine" (lysine) Met M Methionine Phe F "Fenylalanine" (phenylalanine) Pro P Proline

Ser S Serine Thr T Threonine Trp W tWyptophan (tryptophan) Tyr Y tYrosine Val V Valine

Angles (simple, dihedral or torsion), reporting with mouse clicks.

In QuickViews, DISPLAY, Clicks, then check Report angles or Report dihedral (torsion) angles.

Animations.

• For animations in PowerPoint please see PowerPoint.
• Animations, movies, and morphs of conformational changes, thermal motion, etc. can be played in PE in a variety of renderings and color schemes, rotated for viewing from any perspective, and saved for playback outside of PE in Netscape or IE. For details and examples, click on the animated image of an EF hand near the top of the FrontDoor, or go directly to Animations in Protein Explorer (where you will also find a link to morphing methods).
• PE also includes instructions for making animated GIF files (also called multi-GIF files) such as the ones shown here. PE's animation player automatically generates a script that can be executed by RasMol to save the frames for an animated GIF -- see Making an Animated GIF with Protein Explorer. If you know or have time to learn some of RasMol's command language, you can save other kinds of movements into animated GIFs, such as changes in the axis of rotation and zooms. Here are examples of pausing and zooming (be patient, there are pauses of several seconds), changing the axis of rotation, morphing (case 1), and morphing (case 2).

Assessment.

See Student Assessment of Learning Gains from Protein Explorer. See also Visitors to the PE website.

Asymmetric unit.

See Gale Rhodes' Glossary of Terms from Crystallography, NMR, and Homology Modeling.

Atlas of macromolecules

A browsable collection of PDB ID codes, with brief descriptions of the molecules they represent. The Atlas is provided as a companion for the molecular visualization Lesson Plans.

Atomic coordinate file

See PDB file. See also Axes, coordinate.

Axes, coordinate.

Each line in the PDB file that begins with "ATOM" gives the Cartesian coordinates for one atom -- its position in space. The origin of this coordinate system, and the directions of the axes, can be viewed by entering the command set axes on. (The background must be black).

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Back function.

See Undo.

Backbone traces.

For an explanation, go to FirstView and click on backbone trace.

Bare Explorer or Comparator

"Bare" is an obsolete PE term. Please see Empty PE.

Bioinformatics

A brief definition of Bioinformatics that I like is given by Nilges and Linge (Institute Pasteur, France): "Bioinformatics derives knowledge from computer analysis of biological data". It concerns large-volumes of biological information, recently genomic sequences, gene expression data from microarrays, protein-interactions, and three-dimensional ("3D") macromolecular structure, but in a broader sense includes various other sources such as clinical trial data, neural networks, or the scientific literature. Bioinformatics encompasses research with, and applications of such information, as well as the development of the supporting computational methods and tools. Other definitions: NIH; bioinformatics.org.
See Structural Bioinformatics, Protein Structure Bioinformatics Resources and Protein Structure Literature.

Biology Workbench

The Biology Workbench is recommended for preparing multiple protein sequence alignments for use in PE's MSA3D. The MSA3D Tutorial (accessible from the MSA3D page within PE) includes step by step instructions for this use of Biology Workbench.

"Biomolecules"

Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the External Resources window (opened with PE Site Map).

Bonds.

"Bonds" refers to bonds between atoms. Bonds may be either covalent (strong) or noncovalent (weak). The latter include van der Waals interactions, hydrogen bonds, and ionic bonds (such as salt bridges). PE attempts to show covalent bonds as rods between atoms, when the molecule is rendered in balls and sticks, or sticks. However, some strong bonds may not be shown as rods (especially involving metals, or between hetero atoms and protein or nucleic acid), or occasionally bond rods may be shown where only noncovalent bonds exist. Determination of the placement of bond rods is made by Chime. For details, see How Does Chime Determine Covalent Bonds?
Noncovalent bonds can be visualized with the Contacts option of the DISPLAY menu of QuickViews, or with the Noncovalent Bond Finder accessible in Advanced Explorer.

Books about protein structure.

See Protein Structure Literature.

Boolean Logic (in QuickViews)

"Boolean logic" means to apply logical operators to sets (of atoms). For example, in the QuickViews Boolean section (scroll down in the QuickViews control panel to find Boolean) new selections can be and-ed with the previous selection (yielding the subset of atoms common to both sets), or-ed ("+", adding atoms in either set), or subtracted (atoms in previously selected set minus atoms in newly selected set). Similarly, display renderings can be added ("+") or subtracted ("-") from those already showing for the currently selected atoms. For example, to a backbone display, you can add stick renderings for sidechains of selected residues.

Browser, web.

The program used to retrieve hypertext information from the Internet and display it, commonly Internet Explorer or Netscape (see also the full list of PE-compatible browsers). PE works only inside a web browser, and requires a web browser plugin called MDL Chime. PE tests the client's web browser thoroughly for compatibility before starting a session.

Busy, PE, permanently

Few operations in PE should take more than 15 seconds, and for those that are expected to take longer, you will usually be warned before confirming the operation. If PE remains busy (red busy indicator below molecule, to right) "permanently" (more than a minute), there are two possible causes. First, you may be doing a complex operation (such as a Contact-Decorated Surface) on a very large structure (more than 25,000 atoms), possibly on an older slower computer. In this case you may want to wait a few minutes to see if the process completes. The second possibility is that PE has become internally confused. The only way to correct this is to close (quit) your PE session and start a new one. It is usually best to close all browser windows so you also re-start the browser (Quit the browser on Macs). This kind of internal confusion rarely happens more than once per day, even when you use PE for many hours. If you find an operation that reproducibly induces a permanently busy condition, please send the PDB identification code and a description of the operation to emartz@microbio.umass.edu. See also Freezing and Crashing, and Tips & Techniques for using PE effectively.

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Cation-pi interactions

The flat face of an aromatic ring has a partial negative charge due to the pi orbitals. Cationic sidechains (Arg, Lys) or sometimes ligands (including metal ions) often align themselves centered over the faces of aromatic rings. Over one fourth of Trp's in the Protein Data Bank interact with cations, and 99% of significant cation-pi interactions occur within a distance of 6.0 Angstroms (Gallivan & Dougherty, 1999). Cation-pi interactions make a significant contribution to the overall stability of most proteins. Gallivan and Dougherty conclude that "cation-pi interactions should be considered alongside the more conventional hydrogen bonds, salt bridges, and hydrophobic effects in any analysis of protein structure". Cation-pi interactions can be displayed in QuickViews (DISPLAY, Cation-pi), where they are explained in the center help frame. Further information can be found in Advanced Explorer under Cation-Pi Interactions, where there is an Introduction, Gallery & Tutorial for Cation-Pi Interactions.

CGI

A CGI (Common Gateway Interface) program is a program on a server that accepts data submitted by a client browser. This differs from a simple website, in which data (web pages or programs) are sent from the server to the client browser, but never in the reverse direction. Until version 2.76, PE used no CGI. All actions were completed internally within PE, meaning that a downloaded copy of PE could function entirely off-line. Even when running PE from a server, after the first use of any component, subsequent uses run from the local browser cache. However, we were unable to devise a mechanism to save MolSlides correctly without CGI, so in PE 2.76, a tiny CGI program is used to save MolSlides generated within PE. This CGI program is housed at Bioinformatics.Org. See also Security.

Chains

In PE, a "chain" is defined as any polymer of amino acids or nucleotides (protein, DNA, or RNA). Each chain has a one-character "name" (typically A, B, C, etc.). Click on a chain to see its name reported in the message box. A list of all chains and their names is included in the Sequences display, available through the PE Site Map. Polymers of carbohydrates have no backbone trace representation, and are not counted as chains, but rather as hetero atoms ("ligand"). An introduction to the representations of chains as backbone traces is linked to FirstView. See also numbers for how to find out the total number of chains.

The number of chains reported by Chime's "show info" command is usually incorrect, and is hidden in Protein Explorer.

Charge of a protein.

You can see the charge of a protein at any pH by using EMBL's isoelectric point server.

Chime

Chime is a web browser plugin that renders the image of the molecule. PE is, in simple terms, a user interface to Chime, and is wholly dependent upon Chime. PE benefits greatly from the chemical and protein intelligence built into Chime. It is Chime that made it feasible for me to develop PE in a reasonable amount of time, working largely alone. Chime works only on Windows and Macintosh, which limits PE to these platforms, although solutions are available for other platforms, including linux, Irix, etc. Chime is free, in part because it is built upon RasMol. Chime was developed by MDL Information Systems, Inc., largely by Tim Maffett, Bryan van Vliet, and Franklin Adler (none of whom remain at MDL), and by Jean Holt and others. Maffett deserves much of the credit for the design of Chime, for retaining the macromolecular capabilities of RasMol (of little interest to MDL), and for implementing many requests (not on MDL's agenda) that I made. Unfortunately, Chime's source code is not made available by MDL. Chime is included in a commercial chemical database system, ISIS, which is the main revenue-generating product of MDL. Chime can be downloaded from MDL's Chime Site. See also the history of Chime and history of Chime version releases. Jmol has emerged as the best replacement for Chime.

Chime's Menu

Chime has a built-in menu, distinct from the QuickViews menus (and other menus) of PE. It is unusual to need Chime's menu, and it is rather poorly organized and contains no help. In the rare cases where it is useful, the QuickViews help frame will direct you to use it. To access Chime's menu, click on the MDL frank below and to the right of the molecule.

Some operations most easily accomplished with Chime's menu are spotting missing amino acids, listing the names of all ligand/hetero groups, and selecting all cases of one amino acid or nucleotide.

Citation of PE

See Literature about PE.

Classroom use of macromolecular visualization.

See Lesson Plans for Macromolecular Visualization.

Coloring

In order to color portions of a molecule in an arbitrary way, you must first select the desired portions, and then apply a color. For selecting, see selection methods. To apply a color, you may use the COLOR menu in QuickViews. In addition to some complex color schemes, it lists over a dozen plain colors at the bottom. Be sure to read the help after picking COLOR >Help<. If you prefer, you can enter commands. The best way to learn commands is to watch the commands PE sends to Chime after you use the COLOR menu in QuickViews. Here are a few common examples. Separate commands (e.g. select, then color) must be entered one at a time (or delimited with semicolons ";").

• select 22-47:a   then   color red   to color residues 22-47 of chain A red.
• color [x204060]   to color the selected atoms with RGB (red green blue) hexadecimal values 20, 40, 60 (values range from 0 to FF). This is the same as
• color [32,64,96]   where the RGB values are given in decimal (0-255).

Here is a complete guide to colors, including RGB values.

Commands

Commands sent to Chime instruct it how to modify the view of the molecule. The menus and buttons in PE generate commands and send them to Chime. All commands sent to Chime are recorded by the PE Recorder. Also, commands may be entered by hand in the command slot in the frame at the lower left, above the message box. A good way to learn commands it to watch the commands QuickViews sends to Chime, which are displayed in the message box, and try entering variations of them directly. Protein Explorer and Chime understand a superset of RasMol commands. PE includes a document Using Commands, accessible from near the command input slot. There you will find links to the Command Reference Manuals. PE simplifies typing commands with its command aliases. See also scripts of commands.

Comparative modeling

See Comparative ("Homology") Modeling for Beginners. See also structural genomics.

Complexes

For complexes between protein or peptide chains, see Probable Quaternary Structure. See also ligand.

Comparator

A alternate format of PE that provides side-by-side comparison of two molecules (PDB files) with all the same capabilities as the one-molecule version of PE. Rotations with the mouse can be synchronized. Comparator can be invoked empty, or by pre-specifying two molecules. Links and examples are on the FrontDoor. It is also possible to set up a four-molecule comparison. For details, see the fine print under "Manual Adjust" in Window Size Control in PE.

Conservation

See Evolution.

ConSurf Server

The ConSurf Server provides an easy yet sophisticated method for visualizing patches of evolutionarily conserved (or variable) amino acids in 3D protein structures. See its Gallery of Examples, and our gallery of Downloaded Examples. Given only a PDB identification code and specification of a chain, ConSurf proceeds completely automatically. Optionally, you may provide your own atomic coordinates, multiple sequence alignment or phylogenetic tree. The ConSurf server offers visualization of its results in PE using a special ConSurf control panel. Beginning with ConSurf version 3, you can download a customized PDB file that contains the results of a ConSurf job. When this PDB file is loaded into Empty Explorer, the ConSurf control panel will appear automatically (even if the computer is not connected to the Internet). See Downloaded Examples. Alternatively, the ConSurf color scheme can be applied to the molecule in PE by copying the "RasMol coloring script" from the ConSurf Run Results page, and running it in PE. Here is documentation on the interface between PE and ConSurf 3. See also MSA3D.

Control panel

The panel (frame) at the upper left in the main (multiple-frame) PE window containing buttons, menus, and links that control the view of the molecule. PE's Site Map provides an overview of its control panels and enables easy navigation between them. Examples of control panels are FirstView, Features of the Molecule, QuickViews, Advanced Explorer, and from Advanced Explorer, MSA3D: Multiple Sequence Alignment Coloring, Cation-p Interactions/Salt Bridges.

Cookies

PE saves certain information between sessions on your computer. This information includes your preferences, and the ten most recently loaded molecules (in the Select previously loaded PDB file menu on the Load Molecules control panel). The web browser's mechanism for saving such information is called "cookies" for obscure reasons. Here is more information about cookies and cookie safety.

Copyright:

Please see PE Copyright.

Corey, Pauling, Koltun (CPK).

"CPK models" refers to physical, space-filling atomic models with atoms of van der Waals radii, developed in the pre-computer era. These CPK models also had a standard color scheme, similar to the "Element (CPK)" color scheme used in RasMol, inherited by Chime and hence by PE. One difference is that carbon was usually black in physical models, but is gray in PE. The CPK color scheme is incorporated into the DRuMS system of standard color schemes.

Counts of atoms, bonds, chains, residues, disulfide bonds, helices/strands/turns

See numbers.

Covalent bonds

See bonds.

CPK.

See Corey, Pauling, Koltin.

Crashing of Protein Explorer or your web browser.

Resizing PE's window size may cause it to crash -- please see resizing. If your web browser stops responding ("freezes"), or "crashes", close all web browser windows (on Macintosh, you must Quit from the application), restart the web browser, and restart your PE session. This usually corrects problems. On rare occasions, you may need to reboot your computer to fix some strange behavior. See also Freezing, PE permanently busy, and Tips & Techniques for using PE effectively. Netscape and Chime were developed simultaneously, and each has a few bugs that cause occasional problems. This is beyond our control, but it rarely causes a problem more than once or twice a day, even with PE sessions of several hours.

Crystal contacts

Intermolecular contacts that form as as result of protein crystallization are distinguished from specific oligomer contacts. Detailed information is available in the External Resources window (accessed from PE's Site Map) where you will find a link to Crystal Contacts.

Crystallography, X-ray

See Nature of 3D Structural Data.

Cylinders,

as a cartoon rendering of alpha helices, are not available.

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Dates in PDB file headers

PE's Features of the Molecule control panel displays a "deposition date" obtained from the PDB file header. It is the date that the atomic coordinates were deposited at the Protein Data Bank. Other dates available in the header may include revision dates on which the file was modified or a new file was entered as well as the dates of publication of literature references. The Protein Data Bank's Structure Explorer page also shows a "release date" for each entry. This is the date the entry became publically available. Authors sometimes deposit an entry subject to a "hold" condition until a specified date, such as the date of journal publication.

DeepView.

DeepView, also known as SwissPDBViewer, is the best free modeling software package available. It can dock two molecules, structurally align two molecules, mutate PDB files, fill out unit cells and translate them using crystal symmetry, do homology models and energy minimization. The results can be saved as PDB files and explored in PE. DeepView and related resources can be found under freeware at molvisindex.org. PE includes instructions for using DeepView to construct crystal contacts. The best introductions to how to use DeepView are by Gale Rhodes. There is a DeepView section at molvisindex.org. DeepView can be downloaded from www.expasy.org/spdbv.

Discovery in PE

See Discovery in PE, a guide for recording observations.

Disorder.

See temperature value.

Displaying PDB files (molecules).

• For help in finding PDB data files for particular molecules, see Finding Molecules on the FrontDoor.
• If you already know the 4-character PDB identification code, and if you are on-line, you can simply enter the code in the slot on the FrontDoor. Or you can start Empty PE which will take you to the Load Molecules control panel, where you can enter the code.
• To display downloaded PDB files, see Load Molecules.

Distances between atoms, reporting with mouse clicks.

In QuickViews, DISPLAY, Clicks, then check Report distances (in Angstroms).

Disulfide bonds

A disulfide bond is a covalent bond between the sulfur atoms in two cysteine residues (reduced form), forming one cystine (one oxidized cysteine dimer). Disulfide bonds may join two peptide chains (an inter-chain disulfide bond) or two regions of the same chain (an intra-chain disulfide bridge). 1KAL has intrachain disulfide bonds; At the FrontDoor, the Quick-Start link to the Antibody fab:lysozyme complex (1FDL) shows inter-chain disulfides. Schematic diagrams of various renderings of disulfide bonds are available from a link at FirstView. For counts of disulfide bonds, see numbers.

Docking two molecules.

It is not possible to load multiple PDB files into Chime, nor move molecules relative to each other in a single Chime image. This can be simulated, laboriously, with animations of multiple-model ensembles in NMR format. Two molecules can be displayed side by side in Protein Comparator, and moved together in synchrony or independently. Two molecules can be aligned and displayed together, but cannot be moved relative to each other. It is possible to move molecules relative to each other in DeepView or Berkeley-RasMol.

Double molecule.

See multiple molecules.

Downloading

• Downloading Protein Explorer.
• Downloading the Chime plugin. (What is Chime?)
• Downloading molecules, see PDB Files, Downloading and Saving.
• On-line vs. downloaded PE? How to find out which you are using.

Driscoll, Timothy

Author of the PE Recorder. Also authored the Chime shell and much of the content for the Biochemistry in 3D website for Lehninger's Principles of Biochemstry, and for Stryer's Biochemstry. See also DRuMS, the system of color schemes used in PE. Founder of MolVisions.Com.

DRuMS.

A system of standard color schemes for macromolecular visualization used in PE, documented by Tim Driscoll in collaboration with Frieda Reichsman. See the DRuMS Website.

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Electrostatic potential

See molecular electrostatic potential.

"Empty" Explorer or Comparator

Starting PE "empty" means starting it before you tell it what molecule to display. When started "empty", PE shows its "Load Molecule" control panel, which offers several ways to load molecules. There, the last ten molecules loaded can be re-loaded from a pick list. You can start either Protein Explorer or Protein Comparator "empty" from PE's FrontDoor.

Entering a command.

Commands (or command aliases) may be typed in the slot that says "# Commands May Be Entered Here". Pressing the Enter key will then execute the command.

Errors

See Troubleshooting.

Evaluation.

See Assessment.

Evolution

Multiple sequence alignments can reveal patches on a protein surface that are conserved to maintain their functions. The easiest and most sophisticated method to visualize conserved surface patches is with the ConSurf Server. Prior to the release of ConSurf, PE offered MSA3D, which remains available.

Experimental Method

There are several types of experimental data upon which the model in a PDB file can be based. Three principal categories are X-ray crystallography, NMR, and theoretical models (including comparative models). See also Nature of 3D Structural Data.

Expert Mode

In the Preferences, if you check Expert, FirstView will not be shown unless requested, and in general less help and fewer alerts/warnings will be displayed. A complete list of all the effects of enabling Expert Mode is available.

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FAQ

Frequently Asked Questions, see PE's FAQ.

"Features of the Molecule" control panel

PE's Features of the Molecule control panel displays information extracted from the PDB file header. Important information provided by the author(s) of the model is displayed in a more accessible format, with one-click visualization of author-designated substructures, and a link for displaying the complete header text. To get to Features of the Molecule from another control panel, look for the link PE Site Map in the current control panel. You may have to scroll the control panel up or down to find it.

Fewer chains

Methods for eliminating some of the chains from your PDB file are explained in the link to Fewer or Single Chains in the External Resources list (accessed from PE's Site Map); or go directly to Fewer or Single Chains.

Finding PDB files

Please see Searching for 3D molecular structures and PDB files.

FirstView

The control panel titled FirstView describes the first view of a molecule offered by PE. You'll arrive at FirstView automatically whenever you start PE, unless you have checked Expert in Preferences. To get to FirstView from another control panel, look for the link PE Site Map in the current control panel. You may have to scroll the control panel up or down to find it.
FirstView introduces

• chains and backbone traces,
• ligands,
• water and hydrogen,
• hetero atoms,
• color by element (the CPK color scheme),
• disulfide bonds,
• clicking on atoms to identify them,
  and offers the
• 1-Hour Tour
  and questions to structure
• Recording Your Observations.

Technical explanation of the rationale and methods for the FirstView image:

• All protein or nucleic acid chains are displayed as backbone traces. Each chain is given a distinct color.
• All hetero atoms (ligands or solvent) are displayed as spacefilling van der Waals spheres, colored by element.
• Disulfide bonds are shown as yellow rods connecting backbone traces.
• Nothing invisible. No important entity should be invisible. In particular, single-residue "chains" are shown as small spheres (the same diameter as multiple-residue backbone traces). An example is chain B in 1B07.
• Illegally formatted atoms. Any atoms that are not designated as belonging to a standard amino acid or nucleotide (in the PDB format), nor as HETERO, are shown as ball-and-stick, colored by element. Such atoms are illegal in the PDB format but may be common in PDB files obtained from sources other than the Protein Data Bank. Example: the phospholipids in this theoretical model of a hydrated lipid bilayer are given the residue name LIP but not designated HETERO.
• Unknown residues. Atoms in residues named UNK are shown in ball-and-stick, colored by element. Example: in 1SXJ, chain A residues 697-747 are designated UNK because of uncertainty in the sequence register.
• When the PDB file contains multiple models (as for an NMR result, or in a morph animation), only the first model is displayed, rendered the same as for a single-model PDB file, unless Expert mode is checked in Preferences. In the latter case, all models are shown as thin backbone traces, with hetero atoms spacefilled.

The command script that generates FirstView's display can be captured by displaying it in the message box. To do this, click on Control (immediately above the message box), check Initial view of newly loaded molecules, uncheck Keep only 30 lines of messages, click Back, and then use the PE Site Map to Reset View. Block everything in the message box and paste it into a text editor to view it. Note that in Windows (but not Macintosh), messages appear in reverse order (earliest at the bottom and most recent at the top). The order can be changed in Preferences by checking Add new messages at the bottom. This is not the default in Windows because it makes the most recent message always out of view -- restore the default preference when finished!

Free R

Free R is a statistical quantity introduced in 1992 by Axel T. Brünger to assess the quality of a model from X-ray crystallographic data. It is calculated in the same manner as the R value, but from a subset of the data set aside for the calculation of free R, and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced during refinement. As a rule of thumb, free R should not exceed the R value by more than 0.05; that is, if the R value is 0.20, free R should not significantly exceed 0.25. Free R values exceeding 0.40 raise serious doubts about the model. See also Quality of the molecular model.

Freezing of your computer, PE, or your web browser

If your computer gets very slow while you are using PE, see if you have PE sessions (windows) in the background with spinning molecules. Spinning several molecules at once will make your computer very slow, even if you can't see them. Turn off unnecessary spinning, and close PE sessions you don't need. See also Crashing, PE permantly busy, and Tips & Techniques for using PE effectively. Macintosh: Make sure you have given Netscape adequate memory -- see Troubleshooting.

French PE

See PE en Français.

FrontDoor

The first page you see when you go to www.proteinexplorer.org. Links that start PE by pre-specifying a molecule skip the FrontDoor. The FrontDoor provides numerous methods for entering PE, information about PE, and links to other Chime resources.

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Gaps.

See missing residues.

Gecko browsers

Firefox (getfirefox.com), Mozilla (mozilla.org), and Netscape (netscape.com) are open-source web browsers that share a common HTML rendering engine named "Gecko".

Gzipping PDB files

PDB files that are put on a server to be displayed in Chime or Protein Explorer should be gzipped. This reduces their size about 3.5-fold, and the time required to transfer them through the Internet is reduced in proportion. Chime unzips these files automatically and does not take a noticeable time to do so. (If you want your files to be readable by RasMol directly from the server, you should not gzip them, because RasMol does not understand gzipped PDB files. However, if the gzipped file is first displayed in Chime from the server, and then saved from Chime, Chime saves an unzipped version of the file readable by RasMol.) Here are instructions for gzipping, including the program to do it.

Please note that the gzipped format is not the same as some other common data compression formats, such as WinZip. Chime cannot decode a WinZipped file unless it is first decompressed by WinZip.

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Header (of PDB file)

The PDB file header is a block of text at the beginning of the PDB file that precedes the atomic coordinates. The header contains information deemed important by the authors of the PDB file, including the original literature citation, full names of ligands, optionally residues constituting various functional sites, etc. This information is accessible in PE's Features of the Molecule control panel.

Hetero atoms

"Hetero" is a term defined in the PDB file format, and inherited by Chime and PE. It denotes all atoms that are not included in chains of protein or nucleic acid. Thus, hetero atoms include ligands, solvent, metal ions, and all carbohydrate moieties. Hetero atoms may or may not be covalently bound to chains of protein or nucleic acid. Nonstandard amino acids and nucleotides will display as hetero atoms. More information on "hetero atoms" is available at FirstView, and in QuickViews under SELECT Ligand, or SELECT Solvent.

Hiding portions of the molecule

The following strategies can be used in QuickViews to hide portions of the molecule.

• Use the SELECT menu to select what you want to see (or see selection methods). Then DISPLAY Only.
• Select something you want to hide, then DISPLAY Hide. You will be presented with a menu of possible things to hide, including hide everything.
• This is more cumbersome than DISPLAY Only, but you might like to know that after selecting what you want to see, you could SELECT Invert, then DISPLAY Hide.
• Note that DISPLAY Hide offers hide everything, but if you like commands, enter restrict none (or the alias rn) to hide everything. If anything remains visible, it can be hidden with options available on DISPLAY Hide, and you can then observe the relevant commands as they are displayed in the message box.

See also Fewer or single chains.

History.

PE includes a History mechanism for recalling previous molecular views within a session, and returning the session to a previous molecular view. Access this mechanism with the History link beneath the message box. See also undo and saving/restoring a PE session, and the PE Recorder.

For the history of PE, see Purpose of the Protein Explorer, PE's Web Browser Testing mechanisms, RasMol, and Publications about PE.
Also available are a History of Visualization of Biological Macromolecules, the Earliest Solutions for Macromolecular Crystal Structures, and Protein Structure Literature.

Hits to the PE website

See Visitors.

Homology modeling (synonomous with "comparative modeling")

See Homology modeling for beginners. See also structural genomics.

Hyperlinks to PE

It is easy to make a hyperlink that starts PE and automatically displays the desired molecule.

• On-line: http://proteinexplorer.org/pe.htm?id=xxxx where "xxxx" is the PDB ID code for the molecule desired.
• Off-line/local files: Let's assume you have downloaded and installed PE in c:\chime\pe2.0, and you have also downloaded a PDB file and saved it in c:\pdbs\1d66.pdb. This hyperlink will start PE and display the molecule: file:///c|/chime/pe2.0/pe.htm?id=file%3A///c|/pdbs/1d66.pdb

Complete instructions are linked to PE's FrontDoor.

HTML

HyperText Markup Language. The language that specifies how text will be formatted and displayed in a web browser, such as Netscape or Internet Explorer. PE is built with HTML and javascript.

Hydrogen atoms (and water)

Click on Water, and from there on more about hydrogen, starting from FirstView. Or here is a direct link to more about hydrogen. You can add hydrogen atoms to a molecule lacking them by several methods. Note that the two servers below give somewhat different results -- caveat emptor!

• Use the MolProbity: All-Atom Contact Analysis server. Hydrogens are added to both protein and nucleic acids (but not to water). This has the advantage that you also get a unique analysis of the quality of the model, including Gln/Asn/His residues with sidechains that should be flipped, an overall clash score, etc.
• Use Gert Vriend's WHATIF WWW Interface. Hydrogens are added to both protein and nucleic acids (but not to water).
  • Under Server Classes (at left) click "Hydrogen (bonds)".
  • Select "Add protons to structure".
  • Enter your PDB ID or upload a coordinate file.
  • After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.
• You can also use Chime itself to add hydrogen atoms to protein (but not nucleic acid, ligand, or solvent) -- but you cannot save them to a PDB file. Open Chime's menu, and select Options, Sprout Hydrogens. Next, you will need to select them (in QuickViews, SELECT Hydrogen, or SELECT All) and display them. Beware: Chime has been known to make some mistakes in where it puts the hydrogen atoms. Again, using Chime's menu for "File, Save molecule as" will save a PDB file but it will not include these hydrogens. Use one of the other methods above to save a PDB file with hydrogens.

Hydrogen bonds.

Typical hydrogen bond within a protein.

Hydrogen bonds occur when a "donor" atom donates its covalently bonded hydrogen atom to an electronegative "acceptor" atom. The oxygen in -OH (e.g. Ser, Thr, Tyr), HOH, and the nitrogen in -NH₃⁺ (as in Lys, Arg) or -NH- (as in the main chain peptide bond, Trp, His, Arg, nucleotide bases) are typical donors. The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the main chain) or nitrogens with three covalent bonds =N- (as in His, Trp, or nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

Jeffrey categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", 3.2-4.0 Å as "weak, electrostatic" (page 12). Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category, strong hbonds requiring moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey, p. 14). The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey, pp. 191, 200). Since many PDB files lack hydrogen atoms, the presence of an energetically significant hydrogen bond can be inferred when a probable donor and acceptor are within 3.5 Å of each other. PE's DISPLAY Contacts defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens and nitrogens.

At present, PE can display as rods connecting atoms only two subsets of hydrogen bonds: protein backbone-to-backbone hbonds within chains (but not between chains), and Watson-Crick hbonds between DNA base pairs. These can be shown in QuickViews: DISPLAY Hbonds, where further information will be shown automatically. PE presently has no built-in routines to show hbonds between backbone and sidechain, backbone and water, sidechain and sidechain, sidechain and water, protein and ligand, protein and nucleic acid, non-canonical hbonds in DNA or RNA, etc. However, manual methods are available to show arbitrary bonds.

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Internet Explorer (IE) (trademark of Microsoft Corporation)

PE works better in Netscape than in IE -- here are the known differences. Prior to 2002, PE worked only in the Netscape web browser. In version 1.91 Beta, PE was adapted to work in either web browser, with the help of Paul Pillot and Jean-Philippe Demers (see Protein Explorer's Web Browser Testing for Microsoft's Internet Explorer and Netscape Communicator and Protein Explorer's Implementation in Microsoft's Internet Explorer). See also Tips & Techniques for IE-specific tips. (These IE-specific tips display only if you are using IE). If you are having problems getting PE to work in IE, see Troubleshooting.

Irix

Protein Explorer works well in a Microsoft Windows window on SGI/Irix supported by Citrix Metaframe.

Isoelectric point of a protein.

The isoelectric point, or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative charge, and when lower, positive charge. You can calculate the isoelectric point of your protein easily using on-line resources.

1. First, get the one-letter amino acid sequence of your protein. Use PE's Site Map, External Resources to open PDB's Structure Explorer from RCSB. There click on the link (at the left) Sequence Details, and on that page, click on Download all chains in FASTA format. Block the sequence of the chain of interest (excluding the comment line beginning >) and copy it to the clipboard.
2. Second, go to the EMBL WWW Gateway to Isoelectric Point Service, paste your sequence in the box, and press the button.
3. Warning: the sequence you paste in must be in UPPER CASE one letter code. If you paste in a lower case sequence, you'll get pI = 6.014999, which is for the backbone only, because it doesn't recognize lower case amino acids!

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Javascript

The programming language with which PE is built, along with HTML. Javascript is a programming language that works only within the web browser. Javascript is interpreted by the web browser. Basically, it adds programming capability to HTML documents. Javascript should not be confused with java, a general-purpose, cross-platform programming language. In PE, javascript controls Chime by sending it commands. PE comprises over 40,000 lines of HTML plus javascript.

Javascript error(s)

Javascript errors should not occur when running PE, unless you do not have Chime configured properly. In that case, you will never see any molecule in PE, and you need to consult Troubleshooting.
If you are using a Mac PPC, and you have been unable to get PE to display a molecule, and you are getting this javascript error: top-fr_chime.document.form_chime.chime_graphics01 has no properties you can fix it by following the troubleshooting procedure Enabling Chime in Macintosh.
If Protein Explorer did show you a molecule, and then during the session a javascript error occurred, the most likely reason is that Netscape or Chime has become unstable or unreliable. This may happen occasionally while using Protein Explorer and it is usually not your fault (but see Tips and Techniques for using PE Effectively). The solution is simply to close all your web browser windows (on Macintosh, use the File menu to Quit), wait a few seconds, and then restart your web browser and begin a new session of PE. If that doesn't prevent the javascript error, try rebooting your computer. If you get a javascript error reproducibly after the same action, despite restarting your web browser and rebooting, you have found a bug that should be reported. Diagnosis is best done in Netscape rather than Internet Explorer. Type "javascript:" (including the colon) in the location slot of Netscape, and copy the error report into an email. Describe in detail what version of PE you are using, and what actions induced the error. Send the report to yours truly.

Jmol applet

The Jmol applet is a free, open-source, browser java applet that displays rotatable, zoomable views of macromolecules with rendering capabilities similar to those of the MDL Chime plugin upon which PE is built. Example views can be seen at jmol.org. In 2003-2005, Miguel Howard, working as a volunteer, implemented most of the RasMol/Chime command language in Jmol, as well as greatly improving the implementation of Jmol itself. The efforts of Howard and other members of the volunteer Jmol development team have made Jmol the best replacement for Chime. A replacement is needed because MDL has repeatedly declined to open the source of Chime, has done very little development on Chime since 1998, and has announced plans to phase out Chime. Thus, the biochemical community which has grown so dependent on Chime (because of its outstanding capabilities) has no way to maintain or develop Chime.

Journal articles

See Literature about PE or Protein Structure Literature.

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Labels, adding with mouse clicks.

In QuickViews, DISPLAY, Clicks, then check Display labels on atoms.

Lesson plans.

See Lesson Plans for Macromolecular Visualization.

Ligand.

In general, "ligand" usually means a small molecule specifically bound to a macromolecule by noncovalent bonds. In Chime and PE, "ligand" has a somewhat different definition: all hetero atoms that are not solvent. "Ligand" in this PE sense may be noncovalently or covalently bound to non-hetero atoms, namely chains of protein or nucleic acid. For example, both a noncovalently-bound enzyme inhibitor, and an asparagine-linked (covalently bound) carbohydrate adduct qualify as "ligands" in PE. On the other hand, a single standard nucleotide (A, C, G, T, or U) bound to a protein noncovalently does not fall under the term "ligand" as defined within Chime and thus PE, even though it would be considered "ligand" in the more usual, general sense. Moreover, nonstandard amino acids or nucleotides, despite being in protein or nucleic acid chains, will display as "ligand" in PE. In QuickViews, pressing the [Ligand] button shows a short definition and explanation.

You can conveniently list the names of all ligand groups present in your structure with Chime's Menu: Select, Residue. In the resulting submenu, following the 20 amino acids, are listed all ligand (hetero) group names (limited to 1-3 characters in length).

Limitations.

The following limitations exist in Protein Explorer:

• PE cannot show you a 3D structure if you have only the amino acid sequence. You must obtain a PDB file with atomic coordinates before PE can show you the structure. Resources for finding published PDB files are at PE's FrontDoor. If no experimental structure is published, you could try homology modeling.
• The positions of covalent bonds may be shown incorrectly. See bonds.
• No Docking.
• Only a very limited subset of hydrogen bonds can be shown easily.
• There is visualization but there are no modeling capabilities in PE.
• Images are not always high enough quality for publication in journals, but may be -- see printing images.
• Cylinders are not available as a cartoon rendering for alpha helices.
• Rare PDB files contain sequence irregularities, or chain naming irregularities, that are not handled correctly. See details.
• Portions of the contents of some PDB files are not handled correctly by PE. Known cases.
• There are some limitations that are specific to using PE in Internet Explorer.
• Listed elsewhere are some more technical limitations.

The following former limitations in PE have been removed:

• Making a presentation is now easy by using MolSlides.
• It is now possible to save and restore the state of a PE session.
• There is an undo button, and even a full history mechanism for recalling previous views in a session.

Links to PE

See hyperlinks.

linux

Protein Explorer works well in a Windows subsystem running under linux.

Literature

See Literature about PE or Protein Structure Literature.

Load Molecules

PE's Load Molecules control panel allows molecules to be loaded from downloaded PDB files saved to the local disk (press the [Browse] button), from the Protein Data Bank via Internet if you know the PDB identification code, or from a menu of the most recently loaded molecules. To get to the Load Molecules control panel, from the FrontDoor, enter Empty Explorer, and it will appear automatically. Alternatively, from within a PE session, use the PE Site Map link for New Molecule. Finally, from anyplace in PE, enter .l (period plus lower case "L", no space between) in the command entry slot. See also Displaying PDB files.

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Macintosh computer

PE works very well on Macintosh OS X or OS9. Please see PE-Compatible Browsers and Tips for OS X.

Maffett, Tim.

See Chime.

Martz, Eric.

Principal architect and author of PE. Ph.D. 1969 in biology -- until 1997, an immunologist and cell biologist. See his personal page. Self-taught programmer, who (prior to his involvement in molecular visualization beginning in 1995) wrote the first personal bibliographic management system (Bibliofile, 1981-1991, later known as Document Management System for Citations, no longer on the market), and MFI (1992-1995), a freeware data analysis program for flow cytometry.

Menus

In PE, the menu system is QuickViews. There is also a (rarely needed) menu built into Chime.

MEP

See molecular electrostatic potential.

Message Box.

A white box in the lower left frame of PE. The identities of atoms clicked with the mouse are reported here as messages, as are counts of atoms selected and options such as distances or angles between atoms. When you press buttons or use menus in the control panel, commands are generated automatically by PE and sent to Chime. These commands are shown in the message box, along with other messages from PE or Chime, such as the selected atom count after a "select" command.

Method, experimental

See Experimental Method.

Missing amino acids.

Here is an easy way to find out whether all 20 amino acids are present in your structure. Using Chime's menu, Select, Residue. On the resulting submenu, all 20 amino acids are listed. If any are not present, they are gray instead of black.

Missing residues.

Some residues present in the crystal may be missing, leaving "gaps". Perhaps they were not assigned coordinates because their disorder (or "temperature") was too high in the crystal. This is often the case for the ends of chains, or extended surface loops. For more information about possible reasons for gaps or missing residues, open PE's Site Map, and then either Sequences or Seq3D. This will open a sequence display window, where you will find links to Help about missing residues.

Modeling, molecular.

"Molecular modeling" means creating models of molecules, either from experimental data or theory. The resulting "model" is an atomic coordinate file. "Modeling" also means changing the positions or bonding relationships of atoms in existing models, such as by energy minimization, molecular dynamics, etc. "Modeling" is distinct from "molecular visualization" which, strictly speaking, means looking at a structure without modifying it. The best freeware package for macromolecular modeling is DeepView. See also mutation, model quality, and homology modeling.

Model quality

See Quality, Model.

Models, multiple

See multiple models.

Models, theoretical

See theoretical models.

Molecules, displaying & exploring

See Displaying PDB Files.

Molecule name

Available in PE's Features of the Molecule control panel.

Molecular electrostatic potential

"Molecular electrostatic potential" (MEP) refers to the distribution of electrostatic charges (including partial charges) in a molecule. Most often, it is displayed on a solvent-accessible surface of the molecule, as a color scheme (red negative, blue positive, following CPK). Advanced Explorer has a link to Surfaces, where you can apply various MEP color schemes. However, if you plan to use MEP very often, see the Comparision of MEP Renderings for a better solution.

Molecule Information Window

This window ceased to exist with PE version 2.1 in July, 2003. It is superceded by two resources: the Features of the Molecule control panel, and the External Resources window which can be opened from PE's Site Map.

MolSlides

PE offers a way to save rotatable molecular views easily, and annotate them for showing as slides. These are called MolSlides. The can be saved using Chime or Jmol. MolSlides can be viewed without Protein Explorer. MolSlides in Jmol can be viewed in Safari/OSX and Mozilla/linux as well as popular browsers in Windows. Complete information is available within PE at MolSlides.ProteinExplorer.Org. See also Presentations.

Monitor lines, showing distances between atoms, inserting with mouse clicks.

In QuickViews, DISPLAY, Clicks, then check Display monitor lines between pairs of atoms.

Morphs.

See Animations.

Mouse controls.

See

• Labels, adding with mouse clicks.
• Distances between atoms, reporting with mouse clicks.
• Monitor lines showing interatomic distances, inserting with mouse clicks.
• Angles (simple, dihedral or torsion), reporting with mouse clicks.

• Selection by clicking on items with the mouse: see Selection methods.
• Advanced mouse controls (shift keys) for acting directly on the molecular image: To see the complete list of mouse controls, click on the MDL frank below the image to open Chime's menu, then select Mouse, Open mouse control help page.

Movies.

See Animations.

MSA3D

" Multiple Sequence Alignment 3D" is a feature within PE that can color a 3D protein to show regions of conservation or mutation based on a multiple protein sequence alignment. As of December, 2001, it has been superceded by the ConSurf Server, a more sophisticated and automated way to visualize conserved surface patches on 3D protein structures. MSA3D remains available because it is still useful is special situations, such as alignments of only a few sequences. It is accessed from Advanced Explorer.

Multiple models (in a single PDB file).

Multiple models (molecules) can be included in a single PDB file, and displayed in PE, if they are in NMR format. QuickViews displays only the first model. To see other models, from Advanced Explorer, click on the link to NMR Models/Animation. PE can play the models as a movie, or examine them one at a time, or in selected subsets.

Multiple molecules (multiple PDB files).

See Protein Comparator and docking.

Multiple Sequence Alignment

See MSA3D.

Mutation.

"Mutation" means changing one or more amino acids or nucleotides in a protein or nucleic acid chain.

• Regions of high mutational variability in evolution can be identified and visualized in 3D with the ConSurf Server or MSA3D.
• Mutation of a 3D model is modeling, and hence not within the capabilities of PE. However, it is quite easy to mutate a protein 3D model (PDB file) using DeepView, and then explore the result in PE. See Mutating Residues in PDB Files.

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Name of molecule

Available PE's Features of the Molecule control panel.

Netscape (trademark of Netscape Corporation)

PE works better in Netscape than in Internet Explorer -- here are the known differences. Netscape is the web browser that defined the plugin, and LiveConnect, a protocol for communication between the web browser and the plugin. Chime was developed for Netscape at a time when Netscape was used by the majority of people (1995-8). PE was developed in Netscape, and from its first release (version 0.9 in October 1998) through 2001, PE worked only in Netscape. Because Internet Explorer (IE) became the predominant web browser by the new millenium, PE was adapted to work in IE late in 2001, with the help of Paul Pillot and Jean-Philippe Demers (see Protein Explorer's Web Browser Testing for Microsoft's Internet Explorer and Netscape Communicator). In January, 2005, PE was made compatible with the Gecko family of browsers, Netscape 7, Mozilla, and Firefox, with crucial help from Enrique Castro.

Network error

If the FrontDoor of PE changes to "Network error. Unable to request URL from host ...", and the host URL includes "sitemeter", this means two things. First, either you are not connected to the Internet, or the SiteMeter server is down. Second, the only time I have seen this message is when a software package called AdSubtract is installed. Disabling AdSubtract does not prevent this behavior -- you must uninstall it to prevent this. If this is a problem for you, please contact me. If I receive requests, I'll modify the FrontDoor to prevent this.

New features in PE

See version history of PE.

NMR

NMR (Nuclear Magnetic Resonance) is an experimental method used to determine macromolecular structure. NMR experiments yield an ensemble of models, in contrast to the single "best fit" model yielded by most crystallographic X-ray diffraction experiments. Interpretation of NMR data is more commonly subject to major errors than is crystallography. Differences between NMR models may represent actual thermal motion in aqueous solution, or a lack of information adequate to determine the conformation. All models fit the data well, and the first model is usually not the most representative of the ensemble. In some cases, an "energy-minimized" average model is deposited at the Protein Data Bank. An example is 2BBN, a 21-model NMR ensemble of calmodulin binding a peptide from myosin light-chain kinase, accompanied by 2BBM, a minimized average structure.

• Explore 2BBN & 2BBM in Protein Comparator.

(A simple average has unrealistic covalent bond lengths and angles, so these are adjusted by energy minimization software.) PE's External Resources, accessed from the PE Site Map, provides a link to OLDERADO, which informs you which model is most representative (closest to the average) within the ensemble. (For an introduction to NMR, see Nature of 3D Structural Data.) PE can display and facilitate analysis of ensembles of models from NMR experiments. See multiple models and animations. See also quality of the molecular model, the NMR format for PDB files and About Protein Structure.

NMR format for PDB files.

Multiple models can be manipulated independently in PE if they are in the NMR PDB format. This is standard PDB format plus special records (lines) in the PDB file to delimit the models. Here are excerpts from a small example, 1TOS, a 3-model PDB file for a 10 amino acid peptide.

[last line of PDB file header here]
MODEL        1                                                
ATOM      1  N   TRP     1       0.158  -5.942  -1.276  1.00  0.00 
ATOM      2  CA  TRP     1      -0.403  -4.574  -1.286  1.00  0.00 
... many ATOM lines ...
ATOM    140 2HB  ALA    10      -2.166   4.922  -3.932  1.00  0.00
ATOM    141 3HB  ALA    10      -0.442   5.010  -3.496  1.00  0.00
TER     142      ALA    10                                        
ENDMDL                                                            
MODEL        2                                                    
ATOM    143  N   TRP     1      -0.835  -5.964  -1.681  1.00  0.00
ATOM    144  CA  TRP     1      -0.462  -4.793  -0.861  1.00  0.00
... many ATOM lines ...
ATOM    282 2HB  ALA    10      -1.714   5.358  -4.848  1.00  0.00
ATOM    283 3HB  ALA    10      -0.072   5.290  -4.161  1.00  0.00
TER     284      ALA    10                                        
ENDMDL                                                            
MODEL        3                                                    
ATOM    285  N   TRP     1       0.649  -5.556  -1.233  1.00  0.00
ATOM    286  CA  TRP     1      -0.409  -4.525  -1.209  1.00  0.00
... many ATOM lines ...
ATOM    425 3HB  ALA    10      -0.480   5.286  -3.733  1.00  0.00
TER     426      ALA    10                                        
ENDMDL                                                            

The first ATOM line (or HETATM line) for each model must be preceded with a line "MODEL N", where N is the model number (beginning with one for the first model and going up), and end with a line "ENDMDL". The N in "MODEL N" should line up with the element symbol column. See also NMR.

Noncovalent bonds

Noncovalent bonds include (from weaker to stronger) van der Waals interactions, hydrogen bonds, and salt bridges. The cation-pi interaction is also quite important in protein folding and stability. PE's QuickViews provides an overview of noncovalent bonds to any selected moiety with its DISPLAY Contacts option. Cation-pi interactions are not shown there, so be sure to also use DISPLAY Cation-pi. DISPLAY Salt Br. will show the salt bridge subset of noncovalent interactions. Within-backbone hydrogen bonds can be shown as rods using DISPLAY HBonds. Advanced Explorer provides more flexible interfaces for visualizing cation-pi interactions and salt bridges, enabling you to include ligands, and vary the distance criteria. Finally, in Advanced Explorer you will find a link to the Noncovalent Bond Finder. This is useful for a very detailed, bond-by-bond look at the noncovalent bonds to a selected moiety. Beware that with ordinary PDB files, you will not see the noncovalent bonds between neighboring molecules in a protein crystal -- see Crystal Contacts (also available within PE by using the Mol. Info. link).

Nuclear Magnetic Resonance

See NMR.

Numbers (total counts) of atoms, bonds (covalent and hydrogen), chains, residues, disulfide bonds, helices/strands/turns

Click the link Show counts below the Message Box to display the total counts for the molecule currently loaded.

• Atoms: The first number reported in the message box is the number of atoms in protein or nucleic acid chains. The number in (parentheses) is the number of hetero atoms. The sum of these two is the total number of atoms. Remember that for most PDB files resulting from X-ray crystallography, you should multiply by two to estimate the total atoms including hydrogens. See also selected atom count.
• Bonds (covalent): Covalent bonds are usually determined by Chime. (CONECT records in the PDB file [see PDB file format] are ignored, except for certain special cases.) Chime assigns covalent bonds to any two atoms having a distance from each other of less than 1.9 Å. Here is detailed information about bonds.
• Chains: For the definition of "chain" see chains. The number of chains is reported in the Sequences display (available from PE Site Map). (The number of chains reported by Chime's "show info" command is usually incorrect, and so is hidden in PE.)
• Hydrogen bonds: See hydrogen bonds.
• Residues: Residues are called "groups" in Chime. The first number listed after "Number of Groups" is the number of amino acid plus nucleotide residues. The number in (parentheses) is the number of hetero residues.
• Disulfide bonds:Again, Chime assigns disulfide bonds based on proximities of cysteine sulfur atoms (any within 3 Å of each other are deemed disulfide bonded -- SSBOND records in the PDB file are ignored.) The "Number of Bridges" is correct for single-model (most X-ray) files, but might be incorrect (too high) if multiple positions (coordinate sets) are given for some cysteine sidechains. It is incorrect for NMR ensembles of models, because of a bug that assigns bonds between, as well as within, models. See also disulfide bonds.
• Helices/Strands/Turns: For information on the methods used by Chime to assign secondary structure, in QuickViews do COLOR Structure, and read the help in the middle frame.

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Occupancy (crystallographic)

Please see temperature.

Oligomers

Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the External Resources window (accessed via PE Site Map).

One chain

You can hide all but one chain in QuickViews by using SELECT Chain X (where X is the chain that interests you), then DISPLAY Only. Methods for eliminating some of the chains from your PDB file, or getting a PDB file containing a single chain, are explained in the link to Fewer or Single Chains in the External Resources Window (accessed via PE Site Map).

One-Hour Tour

The 1-Hour Tour (formerly called the QuickTour) is the best way for beginners to become familiar with PE. It is available from a link on the FrontDoor, or from links on the FirstView page.

On-line vs. downloaded PE?

To find out whether you are using PE on-line, or from a downloaded copy, at PE's FrontDoor (or any PE page with an address slot), look at the address (URL) in the slot near the top of the browser window. If the address begins with http, PE is coming from a server, and is on-line. If the address begins with file, PE is coming from a downloaded copy. The usual way to start PE on-line is by going to ProteinExplorer.Org, or clicking a link that uses on-line PE. When you are using a downloaded copy of PE, most operations can be done off-line (without an Internet connection).

Off-line vs. on-line PE?

Please see On-line vs. downloaded PE?

OS X, Macintosh

Please see Tips for OS X.

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Papers about PE or protein structure

See Literature about PE or Protein Structure Literature.

PDB

"PDB terms" include:

• Protein Data Bank: PDB stands for Protein Data Bank www.pdb.org, the sole international repository of all published three-dimensional macromolecular structure data (see history of the Protein Data Bank). The Protein Data Bank, founded in 1971 at Brookhaven National Laboratory, USA, was broadened to the World Wide Protein Data Bank www.wwpdb.org in November, 2003.
• PDB identification code: Each molecular structure published at the PDB is assigned a unique four-character code. The first character must be a numeral; the last three characters can be either letters or numerals. Examples: 1d66 (Gal 4 complexed to DNA), 1hho (oxyhemoglobin), 1bl8 (potassium channel).
• PDB file: The data file that specifies the positions in space of every atom in a molecule. The generic name for such a file is an atomic coordinate file. If the file is in PDB format, the filename should end with .pdb to be widely recognizable, including by servers. Published PDB files include, in addition to the atomic coordinates, a header which gives information about the model embodied in the coordinates. Information in the header is accessible in PE's Features of the Molecule. See also Axes, coordinate, Searching for 3D molecular structures, and PDB Files, Downloading and Saving.
• PDB format: One of several file formats for atomic coordinate files. The PDB format is old, ambiguous, and inadequate, but is still the most widely used format because all relevant software can read it. An newer and more flexible alternative format, agreed upon by the International Union of Crystallographers, is mmCIF (macromolecular crystallographic information format). Although mmCIF is offered by the PDB, its use is not yet universal. Chime cannot read mmCIF, but RasMol (version 2.7 and later) can. Here is a short overview of the PDB format. The official format specification is available from the Protein Data Bank under the FILE FORMATS link.

PDB Files, Downloading and Saving

You can save to your hard disk any molecule you see in PE (or Chime on any Chime website). Once you see the molecule in PE, click on "MDL" below the molecule (bottom right corner), and pick File, Save Molecule As. Sources of PDB files are listed on PE's FrontDoor. See also the definition of PDB Files. PDB files that have been saved to your local hard disk can be loaded into PE.

PE

See Protein Explorer.

PE Recorder

See Recorder, PE.

Pedagogy.

See lesson plans.

Peptide bonds (cis, trans).

Peptide bonds are usually planar (consult any biochemistry text), and most have the main chain alpha carbons attached in a "trans" conformation to minimize steric clashes (omega angle 180 degrees). On average, only one peptide bond in 1,000 adopts a "cis" conformation (omega 0 degrees), unless one of the amino acids forming the peptide bond is proline. In the latter case, the frequency is one cis bond out of four. Authors of PDB files may designate cis peptide bonds in CISPEP records, in which case they are identified on the Features of the Molecule control panel.

pI

See isoelectric point.

PiPEs

See Presentations in PE.

Powerpoint (registered trademark of Microsoft).

Although we refer below to Powerpoint, you could equally well use the free Impress presentation software from OpenOffice.Org.

A still snapshot can be copied from PE and pasted directly into a PowerPoint slide. See saving static images.

If you want to rotate, move, or change the image during the presentation, there are several possible solutions:

• The easiest solution is to run both MolSlides, (or PE, or a PiPE) and PowerPoint at the same time. When you get to the point in your presentation where you want to show and rotate the molecule, simply pop the rotating molecular view window in front. To return to PowerPoint, pop its window in front. This method has the advantage that you can do more than simply rotate the molecule -- you have the full power of PE available. Also, the molecule can fill a large part of the screen. This methods works in Safari on Mac OSX or Mozilla on linux with MolSlides saved in Jmol.
  How do I "pop the PE window in front"?
  • Windows: use Alt-Tab to select the PE window, and then again to return to your Slide Show. (This works while you are in SlideShow mode of Powerpoint.)
  • Windows Taskbar: This method is an alternative to the previous one. The Windows Taskbar will be hidden in SlideShow mode unless (before starting your show) you check "Autohide" in Taskbar Properties (right click on a blank area of the Taskbar to get the menu with Properties). Then moving the mouse to the bottom of the screen while showing your slides will pop-up the taskbar in front of the slide. This enables you to pop the PE window in front.
• Another solution is to insert a hyperlink in a PowerPoint slide that starts PE and automatically displays the molecule of interest. This is mostly a convenience in using the previous approach, since (in Windows at least) when you click the hyperlink in your slide, PE starts up but then automatically is pushed into the background, behind the slideshow! So you still have to use one of the above methods to pop the PE window back in front of the slideshow.
• A third solution is to create an animated GIF file, and import it directly into PowerPoint. The advantage is that it is part of your PowerPoint presentation, and you don't have to run PE in the background. (Animated GIF files can also be displayed in web browsers -- here is an example.) The disadvantages are that the only movement possible is the one you animated, typically rotation, and that the image may be smaller than can easily be achieved directly in PE. A smoothly rotating square image 350 pixels on a side can easily exceed several megabytes. Some versions of PowerPoint produce jumpy, irregular animations, especially with large files. To see if your result is optimal, compare it with the appearance of the same animated GIF opened in a web browser.
  • Animated GIF files can be imported directly into PowerPoint 2000 (but not PowerPoint 97): Insert, Picture, From File. Note: dragging the GIF file and dropping it onto the slide will NOT preserve the animation. The animation works only when you show the slideshow (Slide Show, View Show), not while you are composing the slide. If you have PowerPoint 97 (Help, About), you can either upgrade to PowerPoint 2000, or purchase a program to convert animated GIF files to AVI movie files.
  • For methods of creating animated GIF files, see Animations.
• Finally, it is possible to have an interactive rotating molecule directly in a Powerpoint slide (Windows only). This involves using a special Windows plugin, and imbedding a web page (such as a single MolSlides) in a slide. The web page can contain Chime or Jmol. Here are instructions.

Preferences

Click the link Preferences below the message box to see the preference settings. Preferences are remembered between PE sessions. They are specific to the computer upon which they are set (and to the person, if multiple personal profiles have been created in the web browser). Preferences are saved as cookies.

Prerequisites

See Starting PE.

Presentations

To include static images from PE in PowerPoint, please see PowerPoint.

For easy authoring of a series of interactive, rotatable molecular views for projection or as a tutorial, see MolSlides.

To author a series of interactive, rotatable molecular views that can be projected in PE, allowing seamless transitions between the authors' views and self-directed exploration, see Presentations in Protein Explorer

Presentations in Protein Explorer (PiPEs)

PiPEs are an advanced mechanism for authoring tutorials with PE. Before getting into PiPEs, please try MolSlides, which are much easier to author.
PiPEs enable a series of molecular views, designed by the author, to be "played" within PE. Each view can be rotated and zoomed at will, and seamless transitions are possible in both directions between the author's views and the self-directed explorations tools of PE. Please see the extensive documentation on Presentations in Protein Explorer (PiPEs) and the Glossary of PiPE Terms.

Printing publication-quality images.

Molecular images in PE are rendered by Chime, using code developed for RasMol. In writing RasMol, Roger Sayle made an excellent compromise between image quality and speed of interactive rotation of the image. As a result, the images are less satisfactory for publication (see limitations). Often, however, satisfactory images can be obtained for publication by using the largest screen resolution available (e.g. 1600 x 1200 pixels) together with PE, and then saving the image. Here are some publications with figures made by PE.

Software popular for published macromolecular structure images includes Molscript/Raster3D and Pymol. These and other software packages can be found at molvisindex.org. Micheal R. Sawaya has provided a very useful comparision of four such graphics packages, listing pros and cons.

Probable Quaternary Structures (PQS)

Specific oligomers and complete virus capsids can be obtained via PE's link to Probable Quaternary Structures in the External Resources Window (accessed via PE Site Map). This document also provides an introduction to the methods employed and a number of examples. In case there is more than one copy of the molecule in the PDB file due to crystal contacts, a single copy can be obtained from PQS. The European Bioinformatics Institute provides the PQS service.

Problems

• See Specifications for Protein Explorer.
• For problems getting PE to operate, see Starting PE.
• For problems displaying PDB files, see Displaying PDB files.
• See also Limitations of PE, and Freezing or Crashing of your computer or web browser.

Project folders.

Project folders are a feature for advanced users who wish to write command scripts. Project folders (disk directories designated to PE) contain PDB (.pdb) and script (.spt) files that can be loaded and executed in PE. For more information, click the Set Project Folder link below the message box.

Protein Data Bank

See PDB.

Protein Explorer (PE)

Freeware for visual exploration of macromolecular 3D structure. A user interface that makes the power of Chime accessible to students, educators, and occasional users. Easier to use, and much more powerful than RasMol. Independently described as an "impressive integrated knowledge base". Accessible at www.proteinexplorer.org.

See also: PE's control panels, PE's history, PE's Site Map, window size, controlling PE's.

Protein structure

See Nature of 3-D Structural Data, Protein Structure Literature, and Protein Structure Bioinformatics Resources.

Proteome, proteomics

The proteome is "an organism's complete set of proteins in every form they assume" ( PROTEOMICS: High-Speed Biologists Search for Gold in Proteins, by R. F. Service, Science 294:2074, Dec 7, 2001). Proteomics, of course, is the study of proteomes. The number of proteins in an organism's proteome is believed to be roughly an order of magnitude larger than the number of genes in that organism's genome. Proteomics is well funded by pharmaceutical venture capital in the expectation of identifying drug-target proteins. Key methods in proteomics involve identification, particularly in diseased vs. normal states (two-dimensional gel electrophoresis, mass spectrometry), protein interactions (yeast-two-hybrid, protein microarray chips), and structure determination (high-throughput crystallography). For a good overview, see the above-cited article, and others in the proteomics news focus of that issue.

Publications about PE

See Literature about PE.

Publication-quality images, printing.

See Printing.

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Quality of the molecular model

The molecular models published in PDB files for X-ray crystallography vary widely in quality, and rarely they are grossly incorrect. Generally, model quality is indicated by the resolution of the model, the R value, and especially the Free R. Some useful information on model quality, including the Ramachandran plots, can be obtained from PDBReports, linked to Model Quality in the External Resources Window (accessed via PE Site Map). Also linked there is All-atom contact analysis, a new method for finding and correcting errors in crystallographic models. Generally, crystallographic models are reliable in most details when they have resolutions of 2.0 Å or better, R values of 0.20 or less, and R free values of 0.25 or less. However, new and important structural insights are often provided by models with much lower resolution.
NMR models are generally somewhat less reliable than crystallographic models because the method yields less detailed information. For NMR, there are no widely reported global error estimates equivalent to the crystallographic R value and free R. Unlike with crystallographic results, it is not possible to distinguish reliable from unreliable NMR models from information included in the PDB files.
Laskowski has provided an outstandingly clear and succinct overview of how to assess model quality. For examples of published crystallographic errors, see Laskowski, and Kleywegt, 2000, and Kleywegt and Brünger, 1996. Kleywegt has also provided an excellent on-line tutorial on model validation.

Quaternary Structures

Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the External Resources Window (accessed via PE Site Map).

QuickTour

The 1-Hour Tour (formerly called the QuickTour) is the best way for beginners to become familiar with PE. It is available from a link on the FrontDoor, or from links on the FirstView page.

QuickViews

The QuickViews control panel is the heart of the user-friendly exploration power in PE. QuickViews enables you to explore extensively without learning any of Chime's command language. Usually you arrive at QuickViews after FirstView and then Features of the Molecule. To get to QuickViews from another control panel, look for the link PE Site Map in the current control panel. You may have to scroll the control panel up or down to find it. There is also a command to PE that will take you to QuickViews: enter the command .q ("q" preceded by a period).

Quotations about PE

See Literature about PE.

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R value

The R value is used to assess progress in the refinement of a model from X-ray crystallographic data, and can be used as one factor in evaluating the quality of a model (see Free R). R is a measure of error between the observed intensities from the diffraction pattern and the predicted intensities that are calculated from the model. R values of 0.20 or less are taken as evidence that the model is reliable. As a rule of thumb, models with R values substantially exceeding (resolution/10) should be treated with caution. Thus, if the resolution of a model is 2.5 Å, that model's R value should not exceed 0.25. Completely erroneous models (e.g. random models) give R values of 0.40 to 0.60. However, R values themselves must be treated with caution. Unlike the Free R, acceptable R values can be achieved despite serious errors in the model, as demonstrated unequivocally by Kleywegt & Brünger. One famous pitfall that can result in a misleading R value is the addition of substantially more than one water molecule per amino acid. See also Quality of the moleculer model, resolution, the excellent overview by Laskowski, and resources by Gale Rhodes.

Ramachandran plots

As explained in any biochemistry textbook, the main chain (phi and psi) dihedral angles of amino acids in proteins are usually restrained to certain favorable values by steric interactions. The distribution of main chain dihedral angles in a protein model can be visualized in a Ramachandran plot, where the favorable values are designated as "core regions". Models of proteins having substantial numbers of residues (except for glycines, prolines, and D amino acids) falling outside the sterically favorable core regions are suspect. Atomic resolution models (resolution 1.2 Å or better) of good quality have more than 90% their residues in the core regions; models with resolutions of 3.0-4.0 Å generally have about 70% of their residues in the core regions, reflecting the more numerous inaccuracies in such models. See Quality of the molecular model.

Range of residues, selecting, coloring, etc.

To select a range of residues from the sequence, open the PE Site Map, and there open Seq3D. In the Seq3D window, check Show & select range, then click on the first and last residues of the desired range. The residues are now selected, and you can return to QuickViews to change their DISPLAY or COLOR scheme. (If you wish to select more than one range at a time, in Seq3D, check Accumulate selections.)

RasMol

The molecular graphics in PE come from RasMol, a brilliant, stand-alone molecular visualization program written by Roger A. Sayle (see his personal history of RasMol). RasMol is freeware and open-source, thanks to the generosity of its author. Because of that, the RasMol-derivative Chime is free, and because of that (and thanks to the National Science Foundation), PE is free. RasMol is used by millions of people. RasMol and extensive documentation are available from the RasMol Home Page. PE is much easier to use, and more powerful than RasMol.

Recorder, PE

The PE Recorder automatically records all actions from the beginning of each PE session. At any time in a PE session, you can save the current state (as a MolSlide or a command script). These can be played back later to restore the state of a PE session, or can be used to generate a series of molecular views in a set of MolSlides or a Presentation in PE. The controls for the PE Recorder are located below the message box. The PE Recorder also contributes an undo function, and a history mechanism for restoring any earlier view in a session. The PE Recorder was implemented by Tim Driscoll, and designed by Driscoll, Frieda Reichsman, and Eric Martz. See also presentations, saving/restoring a PE session, undo and history.

Reichsman, Frieda

Designed and implemented the flash demonstration movies for PE. Suggested numerous important user-friendliness design features of PE and its Tutorial. Author of content for several major topics in Biochemistry in 3D for Lehninger's Principles of Biochemistry. Founder of Molecules In Motion where some additional high-quality Chime tutorials are available.

Requirements for PE

See Starting PE.

Resizing PE's Window

Resizing PE's window usually causes PE to stop working or crash. This is due to an interaction between the Chime plugin and the web browser that is beyond our control. Therefore, the size of PE's window must be set before the session starts. This is done with a menu on PE's FrontDoor. For details, please see Window Size Control in PE.

Resolution.

X-ray crystallographic models are characterized by a "Resolution" value displayed at PE's Features of the Molecule control panel. (Do not confuse "Resolution" with R Value or Free R.) Small numeric values for resolution mean small uncertainty, hence good resolution; larger values mean poor resolution. For example, 5.0 Å is rather poor resolution for a protein, such that the backbone fold will generally be clear but the sidechains will generally be unresolved. 2.5 Å resolves more atomic positions with greater certainty, including the positions of many sidechains. 1.2 Å is high (truly "atomic") resolution for a protein, where not only sidechains but some hydrogen atoms can be discerned. On average, the uncertainty of the position of an atom is roughly one fifth to one tenth of the resolution for high-quality data (R value 0.20 or less, succinctly explained in Rhodes). However, uncertainty (disorder) typically varies from region to region of the model, and is reflected in the temperature value assigned to each atom.
In NMR results, uncertainty in the position of an atom is represented by the range of positions of that atom in the ensemble of models.

RGB (Red, Green, Blue)

Computer screen colors are made up from light intensities of three primary colors, Red, Green, and Blue (RGB). Hence, any color can be specified as a triplet of RGB intensity values. Usually, each intensity can range from 0 to 255 decimal, which is 00 to FF hexadecimal. PE generates atom-coloring commands and sends them to Chime. The command to Chime that colors the currently selected atoms "DNA-purple" (see DRuMS) is color [xae00fe] (where the initial "x" specifies that the RGB values are hexadecimal). This means "red intensity=AE", "green intensity=00", and "blue intensity=FE". The RGB values are accepted in either lower case (ae00fe) or upper case (AE00FE). Text in an HTML document can be colored with the same RGB values using these HTML tags: <font color="#ae00fe">Protein</font> RGB colors can also be specified and named in PiPEs, where they can be used by name for both atoms and text. See also Coloring Atoms.

Rhodes, Gale

Author of Crystallography Made Crystal Clear, second edition, 1999, a very readable introduction highly recommended for beginners interested in crystallography. See Gale Rhodes' personal website, which has links to many excellent tutorials on molecular visualization and modeling, especially with the use of DeepView.

Rotation troubleshooting.

Dragging on the molecule with the mouse should rotate it. If the molecule fails to rotate, but instead slides without rotating, Netscape and Chime have become corrupted. This is not your fault. The solution is simply to close all Netscape windows (or on Macintosh, File, Quit Netscape). Then restart Netscape and start a new PE session. We hope this doesn't happen to you when you're projecting PE to illustrate a talk -- but it has occasionally happened to us in that situation. Just smile, explain that PE, Netscape and Chime are all under development and hence are not totally bug-free, and proceed by quitting and restarting Netscape. It won't happen again in the same talk, usually.

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Salt bridges

Salt bridges occur between amino acid side-chains with opposite positive or negative full-electron charges, generally when they are 4 Å or less apart (Jeffrey, p. 192). The energetic significance of such complementary charge pairs is a complex function of the local environment and cannot be predicted by Protein Explorer. Putative salt bridges can be displayed by Protein Explorer in QuickViews (DISPLAY, Salt Br.), where they are explained in the center help frame. Further information can be found in Advanced Explorer under Cation-Pi/Salt Bridges, where there is an Introduction, Gallery & Tutorial.

Saving, from PE:

• Static images ("snapshots"), see saving static images or printing publication-quality images.
• Rotating images, see MolSlides (easiest), PiPEs (advanced), or Powerpoint.
• The state of a PE session, see Session, PE, Saving/Restoring.
• Command scripts for Chime, see saving scripts.
• Molecules (PDB Files).

Saving static molecular images from PE. (See also Printing Publication Quality Images.)

Still "snapshot" images are easy to save from PE. Several methods are given below. Once you have saved the still image, you can paste it into any graphics program (e.g. Windows Paint), PowerPoint, or Word. From a graphics program, an image saved in .jpg (jpeg, Joint Photographic Experts Group), .gif (Compuserve Graphics Interchange Format), or .png (Portable Network Graphics) format can be displayed directly in a web page since web browsers understand these image formats. Netscape can save an image from the clipboard to a .jpg file -- see below.

Images saved by the methods listed below are static -- they cannot be rotated. If you want to save the state of your PE session, so you can return to the same image of the molecule easily later, see Saving from PE.

• Copying the image to the clipboard directly from Chime. This method is recommended. First, start a PE session in a window sized so that the Chime image will be the size you desire. After you get the desired image of your molecule, click on the MDL below the molecular image to pop up Chime's menu. Click on Edit, Copy. This copies the image to the clipboard. Now, change to the program into which you wish to paste the image (see above and below), and use Edit, Paste to paste in the image from the (invisible) clipboard.
• Using Netscape to save a .jpg file from the clipboard. Perhaps the easiest (and free) method for saving the image from the clipboard to a .jpg format disk file is with Netscape. After you have completed the previous step (putting the image in the clipboard), in Netscape, File, New, Blank page. (This opens Netscape Composer.) Now Edit, Paste. Your image will appear. (I can't see any way to crop it with Netscape Composer.) Right click on the image, Save image as, and you will be offered to save the image as a .jpg file to a location on your hard disk that you specify. To confirm that the image is on the disk and viewable in Netscape (e.g. for putting on a web server), in Netscape, File, Open Page, Choose File.
• Macintoshes only: saving a selected portion of the screen directly to a file. Get the image you want in PE, in the foreground. Hold down Command (Apple) plus Shift, and press the "4" key. Now, use your mouse to click and drag a rectangle around what you want to save. When you release the mouse, the image will be saved directly to a PICT format disk file. As mentioned above, this will need to be converted into a different image file format if you want do display it in a web browser. Shareware graphics conversion programs are available to do this.
• Windows only: copying the active window to the clipboard. Windows does not provide a built-in method to save a screenshot directly to a file. However, Alt-PrtSc (hold down the Alt key, then press the Print Screen key) copies the active window to the clipboard. If PE is the active window, it will copy the entire PE window. You can then paste the image into any graphics application, or save it using Netscape Composer (see above). Below are given methods for cropping this image. Copying the image directly from Chime (see above) may avoid the need to crop the edges of the image.
• Windows only: cropping an image (free method). Graphics programs typically provide a way to crop the edges off of an image so you keep only the portion in the center that you want. In Windows, this can be done with the free program Paint, that comes with Windows. (Start, Programs, Accessories, Paint.) In Paint, either paste the image from the clipboard (Edit, Paste) or read it in from a disk file (File, Open). In the toolbar at the left, press the Select tool button (dotted rectangle). With the mouse, click and drag to put a rectangle around the portion of the image you wish to keep. Cropping in Paint seems problematic, so here is an easy workaround. With the desired portion of the image selected in the dotted rectangle, Edit, Copy. This places the selected portion of the image on the clipboard, ready to paste into another application. You can now use the Netscape Composer method (above) to save the cropped image to a .jpg file.
• Windows only: saving a selected portion of the screen to an image file. An excellent and inexpensive shareware utility for saving an arbitrary rectangle from the screen into a .jpg or .gif file is PrintKey.
• If you know useful alternative methods or freeware (e.g. for cropping the screenshot in Windows), please email details to me.

Sayle, Roger,

see RasMol.

Screenshots

It is easy to save a screenshot (snapshot of the screen) for your molecule. See Saving static images from PE.

Script Recorder

See Recorder, PE.

Scripts, of commands.

Chime has an extensive command language, a superset of RasMol's command language. PE's menus and buttons generate commands and send them to Chime (using javascript). The commands can be seen in PE's message box. The easiest way to save a script of commands is from the PE Recorder. Scripts of commands can be saved in a plain text file, and run in PE. Alternatively, see the link Set Project Folder beneath PE's message box for another method of running command scripts in PE. Saved scripts can also be used to produce the desired molecular views in a Presentation in Protein Explorer.

Scripts, running ("playing back")

To run ("play back") a command script in PE, first copy the script to the clipboard. Now, click on Import Views.. (below the message box). Scroll down in the Import Views dialog window that opens, paste your script into the box, and click Send Script to PE. Alternatively, see the link Set Project Folder beneath PE's message box for another method of running command scripts in PE.

Scripts, saving.

Command scripts can be saved automatically, then played back in order to restore the currently displayed image. Thus restored, the image is displayed in PE and can be rotated and modified, e.g. with QuickViews.

The PE Recorder provides an easy way to save a command script for restoring a molecular view, or for constructing a presentation of rotatable views.

There is also an older and less satisfactory method to save a command script that is built into Chime. This is mentioned here mostly for the historical record. Click on the MDL frank to the lower right of the molecular image, thereby opening Chime's menu, then Edit, Copy Chime Script. This places the script on the clipboard, from which it can be pasted into any text editor (WordPad in Windows, or BBEdit on Macintosh). The script must be saved as plain text (but with a filename ending .spt) in order to run in Chime. These scripts are unnecessarily long and may take an unnecessarily long time to produce the image -- see Shortening Scripts Saved from RasMol or Chime. These scripts are generated by a mechanism inherited from RasMol which contains a few bugs, and which does not know about surfaces. Hence, they will not generate surfaces, and commands must be inserted manually to restore surfaces.

A command script that is saved to a disk file can be played back in PE: see setting a project folder.

Searching for 3D molecular structures

PE cannot show you a 3D structure if you have only the amino acid   sequence. You must obtain a PDB file with atomic coordinates before PE can show you the structure. Resources for finding published PDB files are at PE's FrontDoor. If no experimental structure is published, you could try homology modeling.

Selected atom count

Chime's rendering (display) and coloring commands always work on the currently selected atoms. Atoms can be selected with the QuickViews SELECT menu, or with commands. After each selection operation, the number of atoms selected is reported in the message box. It is also displayed in a slot below the image of the molecule (except in Comparator).

Security of data when using PE

Proprietary atomic coordinates are safe when explored in PE. Regardless of whether PE is itself coming from a local (proprietary) source, or from a public on-line source such as proteinexplorer.org, the coordinates being explored are never sent out through the Internet by PE itself. PE consists of javascript and HTML code. When PE is provided by a public server, the code is copied into your computer and operated from the web browser's cache. All operations with the atomic coordinate data occur within your computer.

Proprietary MolSlides could be inadvertantly disclosed to a technically sophisticated spy if they are saved by the usual method, which submits them (unencrypted) to the MolSlide Support server at Bioinformatics.Org (or an alternative server; see CGI). To preclude inadvertant disclosure, use a downloaded copy of PE, and save your MolSlides with the off-line method. Disconnecting your computer from the Internet while working on proprietary MolSlides will avoid accidents.

• Beware, however, links to External Resources within PE (available via the PE Site Map). Some of these External Resources require that you submit your coordinates to a server for processing. These include, for example, Probable Quaternary Structure, ConSurf, and MolProbity All-Atom Contact Analysis. If you are using proprietary coordinates, pay attention to whether the address is PE's or that of another server, and don't submit your data to external servers!
• For absolute security with proprietary coordinates, use a downloaded copy of PE and disconnect the network cable from your computer. That way, you won't have access to any external resources that invite you to upload coordinates. (Alternatively, you may have access to a secure intranet that blocks access to public servers.)

Selection methods

Here are some tips on how to select portions of your molecule.

• Choose SELECT, >HELP< in QuickViews. See also Selected atom count.
• To select one ligand among many by clicking on it with the mouse, at QuickViews, SELECT Clicked.
• To select one or a few atoms by clicking on them with the mouse, at QuickViews, SELECT Clicked.
• To select an arbitrary subset of the chains by clicking on them with the mouse, at QuickViews, SELECT Clicked.
  The subset of atoms you select by clicking is automatically saved when you press Stop (stop selecting by clicking). Later, if you choose SELECT Clicked, a new option will appear to re-select that subset.
• To add to (rather than replacing) the selected atoms with the next SELECT menu choice, in the top QuickViews frame, scroll down to Quickviews Boolean Options, and use the pull-down menu there to change the selection logic. Other options there are subtract from, or "and", which selects atoms in common to the new and prior selections.
• To select a range of residues from the sequence, choose DISPLAY Sequences, and then choose Seq3D. (This is also available from the PE Site Map). In the Seq3D window, check Show & select range, then click on the first and last residues defining the range. You may like to save this subset for later re-selection (see below).
• To select all cases of one type of amino acid or nucleotide (e.g. all Trp's or all U's), use Chime's Menu.
• Subsets of atoms you have selected can be saved by choosing SELECT Saved. There, you give each saved set a name of your choice. When the selection process is complicated, saving the result avoids having to repeat the process later in the session. By again choosing SELECT Saved, there will be a menu allowing you to re-select any previously saved set. Saved sets last only until the end of the session, or until you load a different molecule.
• Finally, you can enter commands. The best way to learn commands is to watch the commands PE sends to Chime after you use the SELECT menu in QuickViews. Here are a few common examples:
  • select :a   to select chain A.
  • select :a,:c,:e   to select chains A, C, and E (comma is the same as "or").
  • select 22-47:a   to select residues 22-47 in chains A.
  • select lys,arg   to select all lysines and arginines
  • select calcium or magnesium   to select all Ca or Mg atoms.
  • select oxygen and (asn or gln) and sidechain   to select oxygen atoms in Asn or Gln sidechains.
  Also available is a comprehensive overview of selection commands. Commands can also be used to color or change the display rendering.

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Seq3D

Seq3D is a clickable sequence display that can be used to highlight the locations of particular amino acids or nucleotides in the molecular image. It can also be used to select arbitrary amino acids from the sequence listing (using the option to "Accumulate Selections"), or to highlight and select a range of amino acids (using the option "Show and select range", then clicking on the ends of the range). Seq3D is accessed from the PE Site Map. For a tour of how to use it, see the 1-Hour Tour including the section "Beyond the 1-Hour Tour". Rare PDB files contain sequence irregularities, or chain naming irregularities, that are not handled correctly (details). See also Sequences.

Sequence alignments

See evolution.

Sequences

Amino acid and nucleotide sequences can be displayed by selecting Sequences from the PE Site Map, or in QuickViews with DISPLAY Sequences. Sequences offers a display of sequences with more details, while Seq3D shows a less detailed sequence display, where you can click on residues, or ranges, in the sequence to identify their locations in the molecular image. Rare PDB files contain sequence irregularities, or chain naming irregularities, that are not handled correctly (details).

Session, PE, Saving/Restoring

To Save a PE Session, save a MolSlide by clicking on "Save This View.." below the message box. (For details, see How do I make MolSlides? and Where should I save my MolSlides?). You can save as many molecular views as you wish in a set of MolSlides.
To Restore a PE Session, first import MolSlides by clicking "Import Views.." below the message box. Here are detailed instructions for importing. Next, apply one of the imported MolSlides to your PE session. Here are detailed instructions for applying.

SGI

Protein Explorer works well in a Microsoft Windows window on SGI/Irix supported by Citrix Metaframe.

Show counts

A link below PE's Message Box that displays information there. See Numbers.

Simplified PE?

Some educators have inquired about a "simplified" PE. While PE itself has not been simplified, something in that vein has been provided in MolUSc, but it is available only in French (any volunteers to translate it?). MolUSc is a technically well-documented visualization interface, but without many of the capabilities and the integrated knowledge base offered in PE.

Single chains

Methods for eliminating some, or all but one, of the chains from your PDB file are explained in the link to Fewer or Single Chains in the External Resources Window (accessed via PE Site Map).

Site Map in PE

PE's Site Map is opened by a link in every control panel in PE. You may have to scroll up or down to find the link to the PE Site Map -- it is usually near the cluster of buttons (Spin, Zoom, Water buttons etc.); however, in FirstView, it is at the bottom of the control panel. PE's Site Map has links enabling you to jump to any other control panel, as well as Sequences and External Resources. Thus it provides an overview of all control panels and PE resources, and enables easy navigation within PE.

Size of PE's Window

Please see Window Size.

Slow operations, warnings

Certain operations can be very slow (minutes) if performed when a large subset of atoms is selected in a large molecule. These include toggling the display of water or ligand, DISPLAY Vines, displaying secondary structure with the 2^o button, or using COLOR Polarity or ACGTU. If you request an operation that PE predicts will take more than 12 seconds, you are warned, told that it will be much faster if you first SELECT All, and you are given the option to cancel or proceed slowly. The warning is graded from "slow" to "VERY slow" to "VERY VERY slow" based on the predicted time to completion. The slowness of these operations occurs in Chime's reselection of sets of atoms given names with the define command, when the sets are large. This limitation is beyond our control. For additional technical information, see Design Features: Management of Slow Operations.
The relative speed of Chime is measured in your first session of PE, and saved. You can display it by entering the command speed. If you are curious to know the times PE predicts for requested operations, enter the command speedwatchon.
Mac PPC users only: We have not been able to get PE's measurement of Chime speed to work when PE is downloaded on a Mac PPC. In this case, PE asks you whether you have a G3, G4, or "fast" G4 to estimate Chime's speed. If you prefer, you can use the speed command to report the measured relative speed value when running PE on-line from a server (where the measurement works), and then enter this value for your downloaded copy. To force PE to re-measure (or re-request) the relative Chime speed, enter the command speed and you are given the option to erase the present value. When you start the next PE session, PE will re-determine the relative speed of Chime on your computer.

Snapshots

It is easy to save a snapshot of your molecule. See Saving static images from PE.

Solvent.

In general, of course, the major solvent involved both in protein crystallography and NMR is water. However, in Chime and therefore in PE, the term "solvent" includes, in addition to water, some nonmacromolecular solutes, namely sulfate and phosphate ions, that may be incidentally bound to protein. In PE, all hetero atoms are divided into ligand and solvent. For more information about the definition of "solvent" see "predefined sets" in the RasMol Reference Manual.

Spanish PE

See Protein Explorer en español.

Specifications for Protein Explorer

• For prerequisites for operation, see Starting PE.
• PE requires an atomic coordinate data file, meaning a 3D model of the molecule, usually from X-ray crystallography or NMR (empirical methods), but sometimes a theoretical model.
• Although PE may operate with other file formats, normally atomic coordinate files are used in PDB format.
• PE is a visualization and exploration tool designed for macromolecules, with some quantitative measurement capabilities (distances, angles).
• PE does not do molecular modeling in the strict sense.
• See the section About Protein Explorer on PE's FrontDoor.
• See also Specifications for Presentations in PE, Limitations of PE and History of PE.

Speed, relative, of Chime

See slow operations.

Spin control

By default, the molecule spins at the beginning of a session to show 3D aspects of the structure. It is particularly important when illustrating a lecture or seminar to move the molecule often to help the audience see the 3D structure. Spinning can be stopped or started at will with a "Spin" toggle button, present on every control panel. (You may have to scroll up or down to find the "Spin" button.) Whether or not the molecule is spinning at the beginning of a session is a preference. Starting with PE 2.2, spinning stops automatically, without confirmation, after 3 minutes. (This is to avoid spinning in background sessions, which will degrade computer performance.) Sometimes it is useful to have spinning continue indefinitely. An example is an exhibition display where people walk by. To keep spinning going indefinitely, enter the command alias nss (non stop spin). (Although rarely needed, there is also a command alias nssf for "non stop spin false".)

Starting Protein Explorer

• Prerequisites for PE are a Windows or Macintosh computer with a compatible browser that has MDL Chime installed. See also support for linux/unix etc..
• For diagnosing problems getting PE to start up, look on the FrontDoor for Advanced Startup Options for PE with a checkbox to Start PE step by step.
• For problems getting PE to work, see Troubleshooting and Tips & Techniques for using Protein Explorer (PE) Effectively.
• In general, see methods for Displaying Molecules.
• Methods for displaying downloaded PDB files are listed at the FrontDoor under Downloaded PDB files and Making Hyperlinks that Prespecify Molecules.
• For starting downloaded PE, see the included file named How to Start PE (detailed instructions) and PE Startup (starts PE).

State of PE, saving

Please see Session, PE, Saving/Restoring.

Stereoscopic viewing in three-dimensions

Protein Explorer has a [Stereo] button (on every page after FirstView, near the [Zoom+] and [Bkg] buttons) that toggles split-image stereo on and off. You can control whether the images work with convergent (cross-eyed) or divergent (wall-eyed) viewing in the Preferences. For instructions on viewing stereo pairs unaided, see How can I see the molecule in stereo? An inexpensive, easy to use, pocket-sized viewer for divergent image pairs is available from www.pokescope.com.

Structural Bioinformatics

The subset of bioinformatics that concerns three-dimensional macromolecular structure. Well covered in a 2003 book edited by Bourne and Weissig. See also About Protein Structure.

Structural Genomics

An international initiative begun around 2000 to develop 3D structural models for the majority of proteins in genomes using homology modeling. For details, see the slide on structural genomics (among the slides on Global Protein Structure Issues).

Structure, protein

See Nature of 3-D Structural Data and Protein Structure Literature.

Surfaces

Chime (and hence Protein Explorer) can display surfaces of selected atoms. These are solvent-accessible surfaces that represent the contact path of a sphere rolled around the outside of the cluster of selected atoms. The probe sphere is, by default, 1.4 Å in radius, the size of a water molecule. Surfaces are used in QuickViews DISPLAY Contacts, or DISPLAY Surface. In Advanced Explorer, the Surfaces page enables generation of multiple surfaces concurrently. Here, a variety of color schemes can be applied, including molecular electrostatic potential or molecular lipophilicity potential. Also, the probe radius and spacing, the algorithms used for potential calculations, and the coloring for potentials are adjustable. Michael L. Connolly has provided a detailed on-line Review of Molecular Surfaces.

Synch.

The [Synch] button appears only in Protein Comparator. Moreover, it appears only in Windows; this capability was not implemented in Chime 2 for the Macintosh. When synchronization is turned on with this button, and one molecule is rotated with the mouse, the other molecule will rotate synchronously. In fact, all mouse-controlled operations will be synchronized.

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Teaching molecular structure.

See Lesson Plans for Macromolecular Visualization.

Temperature value (disorder).

Uncertainty in the positions of atoms increases with "disorder" in the protein crystal. Some regions of the molecule may have higher average disorder, and others lower average disorder. Typically, the ends of chains have higher average disorder, and hence their positions are less certain than are residues in the core of a tightly packed domain, where disorder is less.
    "Disorder" has two components. First, some regions of the molecule may adopt different conformations in different copies of the molecule, each molecule's conformation being stable. Second, some regions of every copy of the molecule may be subject to thermal motion, meaning vibration about the rest position (Rhodes). Thermal motion is minimized when the crystal is frozen with liquid nitrogen while being irradiated.
    In the PDB format, each atom is given not only X, Y, and Z Cartesian coordinates, but two additional values immediately following called "occupancy" and "temperature factor" (also known as the "isotropic B value"). If the end of a chain adopts either of two stable positions with equal probability, each position has 50% occupancy. The temperature factor is provided to quantitate the level of thermal motion. However, these two components of disorder cannot be distinguished with crystal diffraction data alone. Therefore, the occupancy is often given as 1.0 (100%), while the degree of "blur" in the electron density map, representing both components of disorder, is reported in the temperature value.
    PE's QuickViews COLOR menu offers a Temperature color scheme, in which the range of temperatures is assigned a spectral sequence from blue (low temperature, higher certainty) to red (higher temperature, higher uncertainty). Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning an positions at all, leading to missing residues.

Theoretical Models

Theoretical models contain far more errors than do models derived empirically from X-ray crystallography or NMR. (See limitations of homology modeling and ab initio modeling.) Although over 800 theoretical models have been deposited in the PDB, the RCSB PDB, as a matter of policy, has segregated them into a separate database. As a consequence, when PE asks for a model from the RCSB PDB by PDB identification code, the request fails. In contrast, the OCA PDB system is configured to return theoretical models by PE's standard request mechanism. Therefore, if you wish to load a theoretical model into PE by specifying its PDB identification code, you must set the PDB mirror URL from which PE fetches PDB files to an OCA mirror, using PE's preferences. By default, PE uses the RCSB PDB. A pretty example of a theoretical model is 1DNN.

Total counts of atoms, bonds, chains, residues, disulfide bonds, helices/strands/turns

See numbers.

Tour, 1-Hour

See One-Hour Tour.

Translations of PE

See Spanish, French.

Troubleshooting

• Can't get Protein Explorer to show a molecule at all? See Troubleshooting your installation.
• Having problems in Macintosh OS X? See Tips for OS X.
• Can't rotate the molecule with the mouse? See rotation troubleshooting.
• The molecule can be rotated with the mouse, but it slides off center when rotating. Zoom down. This is explained in PE's QuickViews, in the middle frame, after you click the [Zoom+] button.
• Did your computer get very slow or freeze while you were using Protein Explorer? See Freezing.
• Did Netscape or Internet Explorer completely stop responding, or crash? See Crashing of Netscape.
• Did you get a javascript error? See javascript errors.
• Are some residues missing in your molecule? See missing residues.
• Did you get a "Network error"? See Network error.
• There is a document on Troubleshooting Presentations in PE (PiPEs).
• Finally, see Limitations of PE.

Tutorial

PE includes an extensive Tutorial.

Two molecules at once.

See Protein Comparator and docking.

 

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Undo.

An Undo button and capability were first provided in PE 2.7 Alpha, released in January, 2005. Pressing the Undo button plays back the command script automatically recorded by the PE Recorder, less the last action. The Undo button is located in the cluster of convenience buttons (including Spin, Zoom, Water, etc.) found on every PE control panel (except FirstView).

Unit cell, crystallographic.

This is the smallest portion of a crystal that, when replicated in three dimensions, makes up the entire crystal. It can be viewed by entering the command set unitcell on. (The background must be black). See Crystal contacts and Axes, coordinate.

Use of PE

See Visitors.

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Validation of molecular model quality

Please see Quality of the molecular model.

Version history of PE

PE includes the history of all released versions, which lists the new features added in each version.

Vibrational dynamics

A protein chain's vibrational dynamics are calculated and animated by the ProMode server.

Virus capsids

Complete virus capsids can be obtained with the link to Probable Quaternary Structures in the External Resources Window (accessed via PE Site Map), provided you have the appropriate virus capsid PDB file loaded.

Visitors to PE

The use of PE is tracked with free meters from sitemeter.com. There is one meter at the bottom of the FrontDoor, and another in a pop-under window invoked when QuickViews is entered. The former measures total interest, while the latter measures visitors who actually install Chime and use PE. If these meters create any problem for you, please let me know and I'll consider other alternatives. See also network errors.

Visualization, molecular.

Strictly speaking, "molecular visualization" means looking at a structure without changing it, that is, without performing molecular modeling.

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Water

For protein crystallography, the protein is crystallized from aqueous solution. In order to preserve the regularity in the ordered array of crystallized protein molecules, the crystal must not be dehydrated -- it is kept moist with the mother liquor from which the crystal formed. Protein crystals are wet and gelatinous. In fact, they are, on average, about half water. For NMR, measurements are made while the protein molecules are in aqueous solution. Here is more information about water.

Web browser

Please see Browser, Web.

Window size, controlling PE's

On the FrontDoor of PE is a menu labeled Window size for new PE sessions. For details on controlling PE's window size, click on that link, or go directly to Window Size Control in PE.

Workshops

Workshops and workshop syllabi to train students, faculty, and researchers in the uses of PE and related resources are available.

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X-ray crystallography

X-ray crystallography is the most common experimental method for determining the 3D structures of macromolecules. About 85% of published macromolecular structures in the Protein Data Bank were determined by X-ray crystallography. For a brief introduction to the method, and references to more information, see Nature of 3D Structural Data. Overall, only a few percent of macromolecular structures selected for crystallography are successfully solved (see the slide on crystallography among the slides on Global Protein Structure Issues). See also quality of the molecular model, temperature value (disorder), resolution, R value, and free R.

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References Cited

• Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.

• Rhodes, Gale, Crystallography made crystal clear, Academic Press, second edition, 1999.

• See also Protein Explorer Literature and General Protein Structure Literature.