[Chimera-users] Atom Specification not working in exported PDB

[Elaine Meng]

Hi Gustaf,
I have every expectation that you should be able to refer to the residue by number, e.g.

show :17
~show :17

…or by atom serial numbers, e.g. (your syntax was wrong):

show @/serialNumber>535 and serialNumber<594

It should be the same as when you have the original trajectory open.  Can you use “show :17” in that case?  We would need an example of your trajectory input to see how Chimera is interpreting it.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 30, 2018, at 4:33 AM, Gustaf Olsson <gustaf.olsson at lnu.se> wrote:
> 
> Hello again Chimera Users
> 
> So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number.
> 
> PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like
> 
>   show :17
>   ~show @536-593
> 
> Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the
> 
>   show :XXX
> 
> works as intended though this affects all residues XXX and I only want to affect residue 17.
> 
> Am I doing something wrong or can I solve this in a simple way?
> 
> Best regards
> // Gustaf