[gmx-users] select in pymol after trjconv

[ZHAO Lina]

On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <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.


>
> 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.

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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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