On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <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. > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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