[Chimera-users] working with PDB files from XplorNIH

[Elaine Meng]

Hi Miriam!
If it’s not a trajectory, you can use the “pdbSegment” attribute in Chimera, for example

sel :1 at N/pdbSegment=A
sel @/pdbSegment=E

The SEGID is supposed to be left-justified in columns 73-76, as in the attached example file test.pdb.

An alternative (which also works for a trajectory) is to use the atom serial number, for example

sel @/serialNumber=684

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Nov 12, 2017, at 1:37 PM, Miriam Gochin <miriam.gochin at tu.edu> wrote:
> 
> I am wondering if it is possible in Chimera to select between different chains in a multimer that are defined by the SEGID parameter in XPLOR.  This appears on columns 77-80 of the PDB file, 
> e.g. in this homotrimer:
> 
> ATOM        1  N   GLN     1       -2.276 -27.488  29.307  1.00  0.00         A
> ...
> ATOM     684  N   GLY     1        4.365 -26.465  20.200  1.00  0.00         C
> ---
> ATOM   1357  N   GLN     1      13.798 -26.207  29.441  1.00  0.00         E
> ...
> 
> Atom selection results in picking up 3 atoms instead of 1, since Chimera expects the chain designation after the residue name.  The XPLOR output is therefore not compatible with Chimera input requirements and I am wondering if there is a workaround.
> 
> Many thanks for any suggestions.
> ---------------------------------
> Miriam Gochin
> Touro University California
> miriam.gochin at tu.edu
> 707-638-5463