[Chimera-users] Symmetric copies of molecules
goddard at cgl.ucsf.edu
Wed Sep 21 16:29:40 PDT 2005
I wrote a Chimera command to show symmetry related copies of a molecule.
As you move the original molecule relative to a density map the positions
of all the symmetry copies are automatically updated.
I tested this with Chimera version 1.2172 just released yesterday.
I don't think it will work with earlier versions of Chimera because of
some function name changes we made.
This archive contains a directory SymmetryCopies that you put in your
Chimera distribution in chimera/share (or on a Mac in
Chimera.app/Contents/Resources/share). Then when you start Chimera
you will have two new Chimera commands "sym" and "~sym".
The symmetry matrices are read from the REMARK 350 BIOMT records in
the PDB file header. Probably you will need to put those matrices in
by hand with a text editor. Below is an example. The matrices represent
the symmetry of the density map. It would make more sense to put them
in the map file header but that is not as easy since it is a binary format
Once you open your PDB file with the BIOMT matrices in the header and
display your density map type
to the Chimera command-line (menu Favorites / Command Line). This
will create copies of the molecule for each symmetry matrix (that is
not the identity). If you freeze the density map by turning off the
checkbutton in the Active column in Model Panel (menu Favorites /
Model Panel) and then move the original molecule with the mouse, all
symmetry copies will be moved using the BIOMT positioning matrices in
the coordinate frame of the density map.
To remove the symmetry copies issue the command:
This is a Chimera convention that tilde in front of a command undoes the
Here are some more details. If you have multiple molecules opened in
Chimera you can specify which one to use in the sym command using the model's
id number listed in the Model Panel dialog. For example
The density map shown in the volume viewer dialog will be used as the
reference coordinate system for applying the symmetries. If you want
to specify which map to use as the reference coordinate system give a
second model id number:
sym #0 #1
If you are showing symmetry for multiple models you can remove the symmetry
copies for just one molecule by giving its model id number with the ~sym
Here is an annoying little problem. If you use the Unshow button on the
volume dialog it removes the density map surface model and forgets its
orientation. The symmetry copies of the molecule will no longer have their
positions updated. Even if you redisplay the map by pressing the Show
button, the symmetry repositioning will no longer work. You'll have to
use ~sym followed by sym to get it working again. If you want to hide the
map you can use the checkbutton in the Model Panel dialog to hide it without
actually deleting the surface, so the symmetry copies will continue to have
their positions updated.
Another problem to look for. Chimera can only handle about 100,000
atoms before it gets slow. Also it uses a few Kbytes of memory per
atom. If you specify alot of symmetry matrices you can quickly create
a large number of atoms. You may need to limit the symmetry matrices
in the PDB header to keep the total number of atoms down.
Let me if this command does what you want. I had fun experimenting with
it. It should make it into a future Chimera release. We plan on making
a production release in early October but have a feature freeze in effect
so it will not be in that release.
Example BIOMT matrices in PDB file 1fav (3-fold axis of symmetry)
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950
REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
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