ZHAO Lina wrote:
On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
========================================
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