- Morphing vs. Toggling. I'll use "toggling" to mean
alternating between two different conformations. If the conformational
differences are small, toggling is sufficient to see the nature of the
changes. When the differences are larger, a "morph" makes it much
easier to see where each portion of the molecule "goes". A "morph"
includes the two empirical conformations plus a series of interpolated
intermediate conformations, played as a "movie". The only technical difference
between a toggle and a morph is the number of models; toggles have 2 models
(usually both empirical), while morphs have more than two. Most of the
methods below apply to both cases.
- What are morph data? Morph data are a series of atomic
coordinate files or "models" each representing a different
conformation of the same molecule. The first and last models are
typically empirically determined, while the intermediates are
- What data format is needed for Chime to display a morph as a
movie? The way I prefer to provide morphs to Chime is in PDB NMR
format ("pseudo-NMR PDB files"). This means simply that each model
(each set of ATOM records which represents one conformation of the
molecule) is preceded with a "MODEL n" record (where "n" is the model
number) and followed with an "ENDMDL" record, all models being in a single
PDB file. The advantage of the PDB NMR
format is that different conformations can contain different atoms.
For example, the binding of calcium to calmodulin can be illustrated
with calcium absent in the first model and present at the last. To see
an example, load any morph in the Protein Morpher, use Chime's menu File,
Save Molecule As to save the PDB file, and examine it in a text editor.
Chime also is able to display movies from data in XYZ format. I
have no experience with XYZ animations. Here is what I have heard
about XYZ format but I cannot guarantee the accuracy of this
information. Chime expects XYZ data to have the same atoms in each
frame, and only the coordinates vary. This allows Chime to handle XYZ
animations faster than NMR animations. I don't believe XYZ allows
designation of residues (amino acids), alpha carbons vs. other
carbons, etc. Thus it is best suited to small molecules.
Examples of XYZ animations
are an alpha helix in thermal motion
and vibrations corresponding to peaks
in an IR spectrum.
- What Chime interfaces display morphs as a movie? The simplest
way to display a morph is with the
Protein Explorer (PE). This interface
is ready to go and needs only the morph NMR PDB file. After loading the
morph NMR PDB file, the PE offers an "NMR Model Selection" control panel.
One option on this panel is an [Auto] button which shows the morph as
a movie, with a user-selectable delay between frames.
The PDB file can be prespecified as a query parameter, so a link
can bring up the Protein Explorer with the movie automatically loading
ready to play. For example
link prespecifies a 14-frame morph of recoverin.
Click on Explore recove14.pdb, then on NMR Model Selection,
then on [Auto]. The movie will play faster if you set the interframe
delay down from the default 0.25 sec to 0.01 sec.
The second option is to use the downloadable template for Chime
presentations. This has detailed documentation on how to build a
presentation. It is possible to insert a toggle or morph as
two buttons in the
A third option is the
Protein Morpher, designed to display
a limited set of morphs, each with some documentation and convenience buttons
not provided in the PE. It can be downloaded,
and a new morph could be installed into it, but this is quite technical
and I haven't written any documentation on how to do this.
In all of the above, the basic strategy is to apply the desired colors
to the models, then show each in turn ("restrict model=N", where "N" is
the model number specified in the MODEL records in the PDB file), and
render it as desired (backbone, spacefill, etc.). If different parts
of the molecule need to be rendered differently, you can use boolean
select commands such as "select model=13 and hetero". More details
will be found in the
Protein Explorer after loading any NMR PDB file with multiple models.
On the "NMR Model Selection" panel, click the help button [?] after
"NMR Model Script".
- How do I align the two conformations? Whether you are making
a toggle or a morph, the first step is to align the two conformations
so that the differences in atomic positions represent only the differences
in conformation. Usually, if the two PDB files are not aligned, there are
large differences in atomic positions resulting simply from different positions
or orientations of the molecules relative to the mathematical origin of
the Cartesian coordinate space. Alignment eliminates these differences
which have nothing to do with conformation.
There are several websites which may provide the alignment you
need. Some of these are mentioned below. Swiss PDB Viewer is excellent
freeware by Nicolas Guex and Manuel Peitsch which can handle all kinds
of alignments very well. Below, I detail one way to do alignments in
Swiss PDB Viewer.
- How do I generate the intermediate
frames from the initial and final PDB files?
First, you may be able to find a ready-made morph at the
Macromolecular Movements maintained by
Mark Gerstein and Werner Krebs at Yale University.
Movie Gallery of Macromolecular Motions, you can click
on the "morph ID", where there is a link to
"Download interpolation as gzip'ped NMR format PDB file",
exactly what you need for Chime.
If you have problems getting these files please contact
the Gerstein Lab for help -- not me.
(For information on gzipping, see the
Martz FAQ at the UMass Chime Resources Site.)
The same group also provides a
Morph Server which will create a morph for you from any two
conformations of a protein. These morphs are "semi-plausible": some
molecular dynamics are applied to the interpolated frames.
However, hetero atoms may not be maintained in these morphs.
If you attempt to use the Yale Morph Server and get an error message
by return email, please contact the Gerstein lab for help. The error
message may not be very specific about the nature of the problem.
Gerard J. Kleywegt
(Uppsala University, Sweden) makes his morph program LSQMAN available
free for academic and non-profit use at his Biomolecular
Morphing site, where you can view his gallery of "chemically reasonable" morphs.
Below, I have provided the programs which I used to make the simple
linear interpolations displayed in the Protein Morpher. The
binaries of these programs operate only under Windows (actually,
- Text Editor. You may need to use a text
editor to edit PDB files. This is any program which can modify the
contents of a text file and save the result as a plain text (ASCII or
DOS Text format). PDB files are plain text. That is, they have no
word processing document formatting codes imbedded in them. If you do
not already know your favorite text editor, here are some options. Simple Text
(Macintosh) or Notepad (Windows) are plain text editors, but they are
not able to handle files as long as most PDB files. Wordpad (Windows)
is fine, but on the first "Save As" be sure to specify "Text document"
on the "Save as type" menu. Then on each subsequent save, be sure to
re-select "Text document". You can also use MS Word or Wordperfect,
but be sure always to save as plain text (also called ASCII or DOS
- PDB files. You may need to be somewhat familiar with the
format and contents of
PDB files. Each line of a PDB file
is called a "record", and the type of information it contains
is specified in the first word in the line. The most important
records for morphing are ATOM records which specify the positions
of the atoms making up the main chain of a protein or nucleic acid.
There may also be important atoms in HETATM records, such as metal ions,
water, ligands, or carbohydrate.
PDB Tools. You may need to use some of the
PDB manipulation programs specified below. These are available
as DOS EXE files which will run in a DOS window under Windows.
If you do not use Windows, you may be interested in the C language source codes
which are also provided. These PDB tool programs are available
III. Preparation of Initial and Final PDB Files
- Select the PDB files representing the initial and final states.
The structures to be morphed must contain identical numbers of residues
(amino acids or nucleotides). For linear interpolation, there must
be an atom-by-atom match in the intial and final states. For Gerstein's
morph server, a few amino acids can differ. In this case, the
amino acids present in the final state will be substituted for any which
differ in the initial state.
- Your initial and final PDB files must each contain exactly one
copy of the structure you wish to morph. Some PDB files result from
crystals which have more than one copy of the molecule in the
asymmetric unit. This will be obvious when you view such a file in
RasMol or Chime. In this case, you must copy the PDB file, giving it a
new name, and in this copy, delete everything except the ATOM and
HETATM records which make up one instance of the structure you wish to
If you need to extract one molecule from a crystallographic PDB file,
and you wish to preserve water, the easiest method is with RasMol.
Select the molecule of interest and the proximal water, then save a
PDB file. RasMol saves only the selected atoms (see
PDB Tools for details of what various programs save when writing
PDB files). Typically, you may wish only water within 3.5 Angstroms
of protein (which would be the first layer of hydrogen-bound water).
If the molecule of interest contained chains A and B, the commands
in RasMol would be:
select within(3.5, (:a or :b))
save pdb <filename>.pdb
- Hetero atoms. Gerstein's server will strip out hetero atoms
(see below for how to restore them). For linear interpolation,
you may include HETATM records in the initial and/or final states.
However, you must be sure they are in the same order. Otherwise,
a water or metal ion may zoom across the molecule, rather than staying
in its proper place, because you have mapped the initial HETATM to
a different final HETATM.
IV. Alignment Methods
If you use the Gerstein & Krebs Morph Server, it does the alignment
for you, and you can skip this section.
If you are particularly interested in the conformational changes
of a small portion of the molecule, such as an active site, it may
be preferable to align just that portion, rather than the entire
molecule. If there are conformational changes in distant parts
of the molecule, whole-molecule alignment may cause the portion
of interest to translate or rotate an a manner unrelated to
conformational changes within that portion. The best way to find
out is to do both kinds of alignment and compare the results.
- Shindyalov and Bourne have provided a Combinatorial Extension alignment
server. Here you can submit any two chains in PDB files and receive the
aligned coordinates in PDB NMR format by selecting the Download
link. Optionally, you can specify a limited range of residues to
align, such as an active site. This method is very fast and convenient
but has possible disadvantages. It aligns only single chains, whereas
the Deep View method below can do multiple chains. It discards ligands,
water, and hetero atoms, whereas the Deep View method below optionally
can retain them.
The PDB file you download from this site is ready to view and toggle
in the Protein
Explorer. For a morph, use the text editor to split the
aligned models into two separate PDB files, and proceed to the
Morphing Methods section below.
- Deep View (formerly known as Swiss PDB Viewer). Using the Deep View
freeware program (DV), align the alpha carbon backbones.
These instructions are for DV version 3.5 beta 1.
- Run DV. If you want to keep water, select Preferences, Loading Protein,
and UNCHECK Ignore solvent.
- Use File, Open PDB file to open the initial PDB file.
Accept the default Rendering Attributes.
Immediately (being careful not to move the image with the mouse!),
UNCHECK the the checkbox labeled "can move" near the top of the
Control Panel. This prevents you from inadvertantly moving the
molecule. (If the Control Panel is not visible, use the menu Display,
Show Control Panel.)
- Now open the second PDB file, the one which represents the final
In the next few steps, we'll align, then save the aligned molecules.
Between alignment and saving, you must not move the aligned molecule with
the mouse. If you do move it, just re-do the alignment before saving.
- Often you can proceed immediately, using Tools, Magic
Fit. After running this, check which groups DV chose to align,
shown red in the control panel. If these are not optimal, use Fit
Molecules from selection (next step below). (To change which molecule
is displayed in the control panel, click on the name of the first
molecule just below the title "Control Panel" at the top -- a menu
will open allowing you to select the second molecule.)
- For more control over the alignment, select identical numbers of
residues in each molecule, then use Tools, Fit Molecules (from
selection). You can select an entire chain by clicking on its
chain letter. Selected residues are shown red, allowing you to verify
what is selected. To select more than one chain, hold down Ctrl while
clicking on additional chain letters. To deselect individual residues,
hold down Ctrl while clicking on the amino acid name. To deselect a
range of residues, hold down Ctrl, click on the first and drag to the
last. To deselect everything (to start over with adding selections)
hold down Shift while clicking on any chain letter.
- After either a Magic fit, or a Fit from selection, calculate the RMS
deviation: Tools, Calculate RMS. You may wish to note this value as
well as the number of atoms used in the alignment.
- On the File menu, UNCHECK Save in original orientation.
This is necessary to allow you to save the second molecule in its
new aligned position.
- Now use File, Save, Project to save both molecules into
a single PDB file.
- Insert a line with "MODEL 1" before the first ATOM record of the
first molecule. The "1" should line up with the element designation, like
ATOM 16 N GLY E 1 48.960 33.944 42.010 1.00 17.00
- Insert a line after the last ATOM or HETATM record of the first
molecule with "ENDMDL", followed by another line with "MODEL 2".
Insert an "ENDMDL" line after the last ATOM/HETATM record of the
- Optionally you may delete all lines except MODEL, ATOM, HETATM,
ENDMDL. Notably, you may delete all SPDV and CONECT records, which
are ignored by Chime anyway.
- The aligned PDB file is now ready to load into the
and view as a toggle.
- To simplify the file by removing hydrogens or removing all atoms
except alpha carbons, see the end of the following section.
- To proceed with morphing, use your text editor to save each molecule
into a separate file (just the ATOM and HETATM records).
V. Morphing Methods
None of the methods below attempt to predict the actual trajectory
of conformational change. Rather, the goal is to allow the eye to
connect the positions of various moieties during the conformational
change, thereby visualizing the changes in contacts and positions
of each moiety.
The simplest method for interpolating intermediate frames between
the initial and final models is linear interpolation. Each atom
is moved in a linear path from its initial to its final position
in equal increments. The resulting intermediate frames are chemically
unrealistic, because atoms may occupy the same space, and bond angles
and distances will not be realistic. Nevertheless, linear interpolation
does allow the eye to connect the positions of any given moiety as the
morph movie runs.
A more sophisticated morph involves application of molecular dynamics
to each frame of the linear interpolation. The resulting chemically
possible frames are described by Gerstein and Krebs as "semi-plausible"
and by Gerard Kleywegt at "chemically reasonable".
In the past, the Gerstein and Krebs Morph Server discarded all hetero
atoms. The results are sometimes rather jerky -- atoms don't necessarily
move through a smooth trajectory, but neither do they move through each
other like ghosts (which they may do in a linear interpolation).
These programs are accessible through the
- Linear Interpolation
- The ready-to-run programs provided for this method operate
only on Windows. These programs are part of my
PDBTools package. (C source code is included so the programs
could be adapted to other operating systems.)
- After you download the PDBTools, unpack them by double-clicking
on the pdbtools.exe file in Windows Explorer. Next, you must either
put the .exe files on your path, or else do your work in a
folder containing them.
- You need to prepare two PDB files representing the initial and final
conformations. These must have exactly the same number of atoms, in exactly
the same order. They must be aligned. Put them in the same folder as the
PDBTools programs. If one file contains hydrogens, and the other doesn't,
or if both do, you can use the program striph.exe to remove
- To make a concrete example, let's assume your initial and final PDB files
are named initial.pdb and final.pdb, respectively, and that you want a 12-frame morph
(10 interpolated frames plus the initial and final frames).
Open a DOS window, type this command at the DOS prompt, and press Enter.
morph2 initial.pdb final.pdb 10
- If there are moieties (typically hetero atoms, or a bound peptide)
present in only one of the initial or final PDB files, they must be removed
in order to make the morph, but after the morph, they can be manually
edited back into the initial or final model as appropriate.
- Rename the output file (morphout.pdb) to a name of your choice.
This file can be
played as a morph "movie" by any of the methods mentioned above
What Chime interfaces display morphs as a movie?. Immediately,
you can open your morphed pdb file in the
and play it as a "movie" in the NMR Model Selection panel with the [Auto]
- If you are only interested in the backbone, you can make the morph
file much smaller by eliminating all atoms except alpha carbons. Do this
with the PDBTools program alphac.exe.
VI. Playback Scripts for Toggles & Morphs
As mentioned above, you can play 2-model PDB files as toggles, and multiple-model
PDB files as movies in the Protein Explorer as is. This section tells how
to put playback buttons in a custom Chime presentation.
Let's take as an example an NMR format PDB file containing two aligned models.
We'll call this file toggle.pdb, but of course you can give it
a more specific name.
Chime presentation template, you can make buttons which will toggle
your models as follows.
- First, you need to have a button which loads toggle.pdb and colors and
renders it suitably. This button will show the two models overlayed.
For instructions on how to make such buttons and scripts, please
Presenting RasMol-saved scripts in Chime.
- Next, you can make a Toggle button
by having it run the following script:
Of course you can use any rendering you wish. If you need to render different
parts differently, see the help button [?] following "NMR Model Script"
on the Protein Explorer's NMR Model Selection panel. The "0.3" values
represent seconds, and can be adjusted to provide the timing you prefer.
- The above script runs as an infinite loop. To stop it, you need another
button in your Chime presentation labeled Stop toggling, which should
send a single script command:
This script must be exactly as shown (no semicolon, comment, or other
- If you have an N-model morph file, you can play a morph movie in
the Chime presentation template simply by expanding the above script
to include a restrict command block for each model, 1 through N.
Use a delay after blocks 1 through N-1, and a loop command after block N.