[gmx-users] select in pymol after trjconv

[Justin A. Lemkul]

ZHAO Lina wrote:
> 
> 
> On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     ZHAO Lina wrote:
> 
>         Hi,
> 
>         after added ions, I got a solv_ions.gro.
> 
>         I use trjconv
> 
>         to produce the solv_ions.pdb
> 
>         when I view it in pymol.
> 
>         I showed sequence,
>         it like
> 
>          1      2   3   4   6
>         ODOAOEOROHODOGOOYE
> 
>         But the solv_ions.pdb looks pretty regular.
> 
>         my problem is that,
> 
>         how could I choose the protein parts.
> 
>         I tried the select protein, resi 1-48
>         some waters are inclusive.
> 
> 
>     Do you have a very large system?  If so, PDB format can only handle
>     a fixed number of digits in the residue and atom numbering fields,
>     so the numbering of your waters restarts from zero.  Such is the
>     limitation when dealing with .pdb files.
> 
> 
> Kind of large.
> I was wrong before, the newly-produced solv_ions.pdb is not regular.
> Before those chains numbered in sequence.
> now different chains numbered from 1-48 1-48 again, former is 1-96 in .gro.
>  

I'm guessing you have different chain identifiers, i.e. identical chains, just 
labeled A and B or something?

> 
> 
>     If you just need to make selections in PyMOL, strip the water out of
>     the file first.
> 
> 
> It's short, the protein part, I did it manually, but the "show cartoon" 
> failed to show all, only show first 1-48.
> 
> I guess I gotta modify the .pdb a little.
> 

Or select by chain rather than residue number, if my theory above is correct.

-Justin

> Thanks for your answering.
> 
> lina
>  
> 
> 
>     -Justin
> 
> 
>         Thanks for any suggestion.
> 
>         lina
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================