[gmx-users] select in pymol after trjconv
lnzhao99 at gmail.com
Mon Mar 7 15:23:40 CET 2011
On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> ZHAO Lina wrote:
>> 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
>> 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.
> 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.
Thanks for your answering.
> Thanks for any suggestion.
> 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
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