[Chimera-users] (no subject)

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 4 14:51:33 PST 2007

Dear Julien,
It is difficult to answer without knowing more about your situation,  
but I will describe what can be done in Chimera.

The "write" command creates one PDB file containing atoms from one  
model ID number.

If you opened your 500 structures from 500 separate PDB files, they  
will have 500 different model ID numbers (#0 #1 #2 ...), so "write"  
cannot be used to combine them.

However, if you opened the 500 structures from a single PDB file,  
where MODEL/ENDMDL records are used to indicate the start and stop of  
each structure, they will be opened as submodels but with the same  
model ID number (#0.1 #0.2 #0.3 ...).  For examples of this single- 
file input, see any NMR structure ensemble from the Protein DataBank,  
such as 1plx. In this single-file case, you can select any set of the  
submodels and write their coordinates to a single PDB file with  
"write" and the "selected" keyword:

open 1plx
select #0.1 #0.3 #0.5
write selected 0 1-3-5.pdb
select #0.2 #0.25
write selected 0 2-25.pdb

(1) you still need to do a separate selection and write command for  
each pair;  depending on how many pairs you planned to write, you  
might want to write a script to create the Chimera script.
(2) the written files will still contain the MODEL and ENDMDL lines  
for submodels for which no atomic coordinates are included, which you  
might want to remove depending on what you are going to do with the  
files. The effect of not removing them is that when you open the file  
later in Chimera, it will still say there are 80 submodels (or  
whatever the total number you started with was) in the Model Panel  
even though some contain 0 atoms.   The display will only show the  
coordinates you wanted, however.

Given these issues, you might prefer to use your own scripts.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 4, 2007, at 1:24 PM, Julien Orts wrote:

> Dear Chimera people,
> I would like to save a lot of pdb. I have for example 500 pdb.
> Each saved pdb file should contains 2 pdbs of these 500 pdbs.
> I can write a script for this but the command
> write does not work for more than two pdb.
>   Is there any other way?
> thank you
> Julien

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