[gmx-users] select in pymol after trjconv

[Justin A. Lemkul]

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.

If you just need to make selections in PyMOL, strip the water out of the file first.

-Justin

> Thanks for any suggestion.
> 
> lina
> 

-- 
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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

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