[gmx-users] select in pymol after trjconv
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. Thanks for any suggestion. lina -- gmx-users mailing listgmx-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
Re: [gmx-users] select in pymol after trjconv
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 listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] select in pymol after trjconv
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 -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 listgmx-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
Re: [gmx-users] select in pymol after trjconv
ATOM397 N ALA48 35.480 52.940 57.920 1.00 0.00 ATOM398 H ALA48 34.740 52.570 57.360 1.00 0.00 ATOM399 CA ALA48 36.190 54.120 57.430 1.00 0.00 ATOM400 CB ALA48 35.900 55.320 58.350 1.00 0.00 ATOM401 C ALA48 37.690 53.840 57.260 1.00 0.00 ATOM402 O1 ALA48 38.120 52.590 57.580 1.00 0.00 ATOM403 O2 ALA48 38.460 54.860 56.810 1.00 0.00 ATOM404 N ASP 1 7.960 12.190 74.660 1.00 0.00 ATOM405 H1 ASP 1 8.090 11.710 75.530 1.00 0.00 ATOM406 H2 ASP 1 7.210 12.840 74.760 1.00 0.00 ATOM407 H3 ASP 1 7.730 11.520 73.950 1.00 0.00 ATOM408 CA ASP 1 9.190 12.900 74.290 1.00 0.00 ATOM409 CB ASP 1 10.390 11.940 74.180 1.00 0.00 ATOM410 CG ASP 1 10.860 11.380 75.510 1.00 0.00 ATOM411 OD1 ASP 1 10.420 11.850 76.560 1.00 0.00 ATOM412 OD2 ASP 1 11.880 10.480 75.450 1.00 0.00 ATOM413 C ASP 1 9.000 13.630 72.970 1.00 0.00 ATOM414 O ASP 1 8.580 13.010 71.990 1.00 0.00 I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain info. Do you have some nice way to view .gro in pymol. (compare VMD I am a bit familiar with pymol) Thanks again, lina -- gmx-users mailing listgmx-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
Re: [gmx-users] select in pymol after trjconv
ZHAO Lina wrote: ATOM397 N ALA48 35.480 52.940 57.920 1.00 0.00 ATOM398 H ALA48 34.740 52.570 57.360 1.00 0.00 ATOM399 CA ALA48 36.190 54.120 57.430 1.00 0.00 ATOM400 CB ALA48 35.900 55.320 58.350 1.00 0.00 ATOM401 C ALA48 37.690 53.840 57.260 1.00 0.00 ATOM402 O1 ALA48 38.120 52.590 57.580 1.00 0.00 ATOM403 O2 ALA48 38.460 54.860 56.810 1.00 0.00 ATOM404 N ASP 1 7.960 12.190 74.660 1.00 0.00 ATOM405 H1 ASP 1 8.090 11.710 75.530 1.00 0.00 ATOM406 H2 ASP 1 7.210 12.840 74.760 1.00 0.00 ATOM407 H3 ASP 1 7.730 11.520 73.950 1.00 0.00 ATOM408 CA ASP 1 9.190 12.900 74.290 1.00 0.00 ATOM409 CB ASP 1 10.390 11.940 74.180 1.00 0.00 ATOM410 CG ASP 1 10.860 11.380 75.510 1.00 0.00 ATOM411 OD1 ASP 1 10.420 11.850 76.560 1.00 0.00 ATOM412 OD2 ASP 1 11.880 10.480 75.450 1.00 0.00 ATOM413 C ASP 1 9.000 13.630 72.970 1.00 0.00 ATOM414 O ASP 1 8.580 13.010 71.990 1.00 0.00 I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain info. Do you have some nice way to view .gro in pymol. (compare VMD I am a bit familiar with pymol) Renumber using genconf. You should be able to select consecutive residues in this way. Otherwise, use a couple quick text editor tricks to write in chain identifiers to make selection easy. -Justin Thanks again, 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 listgmx-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
Re: [gmx-users] select in pymol after trjconv
On Mon, Mar 7, 2011 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain info. Do you have some nice way to view .gro in pymol. (compare VMD I am a bit familiar with pymol) Renumber using genconf. You should be able to select consecutive residues in this way. Otherwise, use a couple quick text editor tricks to write in chain identifiers to make selection easy. genconf works so perfect here. Thanks again! lina -Justin Thanks again, 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 listgmx-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 -- gmx-users mailing listgmx-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
