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 (Asp, Glu) 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.