From: Hally S. <gt...@ma...> - 2008-01-23 18:12:10
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I installed pymol onto a linux system. I can open the program, open the pdb file, and open a .pse file, but I cannot open the .pml file which contains the manipulations that I've already made. Any suggestions? -- Hally Shaffer <>< Graduate Student Georgia Institute of Technology School of Chemistry and Biochemistry gt...@ma... |
From: Justin L. <j.l...@fz...> - 2008-01-23 19:35:58
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type @yourpmlfile.pml Hally Shaffer schrieb: > I installed pymol onto a linux system. I can open the program, open the pdb > file, and open a .pse file, but I cannot open the .pml file which contains the > manipulations that I've already made. Any suggestions? > > -- > Hally Shaffer > <>< Graduate Student > Georgia Institute of Technology > School of Chemistry and Biochemistry > gt...@ma... > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Dr. Sebastian M. Schmidt ------------------------------------------------------------------- ------------------------------------------------------------------- |
From: Hally S. <gt...@ma...> - 2008-01-23 19:53:45
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On a Windows system, I have used the @filename.pml command and that works. I believe I've done what you say on linux, but let me explain what I do. First, I open a blank program through commands in the terminal. This can only be done in the pymol directory. Once that is open, I am able to open pdb files or .pse files by using the File-->Open selections and choose my file from any directory. When I try this for my .pml file, the pymol command window says that it loaded, but nothing shows up in the graphics window. If I try to type @filename.pml in the command line, it gives an error saying it doesn't recognize the name. -- Hally Shaffer <>< Graduate Student Georgia Institute of Technology School of Chemistry and Biochemistry gt...@ma... Quoting Buz Barstow <bu...@ma...>: > Hi Hally, > > Sometimes if you type @ followed by the name of the pml file, you can > get more luck than if you simply type run followed by the name of the > pml file. I don't know why this works, but it's been working a lot for > me recently. > > Good luck! and all the best, > > --Buz > > > On Jan 23, 2008, at 1:12 PM, Hally Shaffer wrote: > > > I installed pymol onto a linux system. I can open the program, open > > the pdb > > file, and open a .pse file, but I cannot open the .pml file which > > contains the > > manipulations that I've already made. Any suggestions? > > > > -- > > Hally Shaffer > > <>< Graduate Student > > Georgia Institute of Technology > > School of Chemistry and Biochemistry > > gt...@ma... > > > > > > > > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > |
From: <li...@ul...> - 2008-01-23 21:58:06
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On Wednesday 23 January 2008 20:53:44 Hally Shaffer wrote: > On a Windows system, I have used the @filename.pml command and that works. > I believe I've done what you say on linux, but let me explain what I do. > First, I open a blank program through commands in the terminal. This can > only be done in the pymol directory. Once that is open, I am able to open > pdb files or .pse files by using the File-->Open selections and choose my > file from any directory. When I try this for my .pml file, the pymol > command window says that it loaded, but nothing shows up in the graphics > window. If I try to type @filename.pml in the command line, it gives an > error saying it doesn't recognize the name. -- It will probably be necessary to use the "cd" command on the PyMOL command line to change to the appropriate directory containing the .pml file. Or you can specify the full path from the current directory to the .pml file after the @. You can find out PyMOL's current working directory with the "pwd" command (pressinf <Escape> to toggle between the graphics view and the text output to see the result). Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel |
From: Tsjerk W. <ts...@gm...> - 2008-01-24 08:38:30
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Hi Hally, It's worthwhile getting on terms with Linux. You mention you start a "blank program" suggesting to me you're starting pymol without anything to be loaded ("pymol"). It's not true that this can only be done in the pymol directory. You can do it anywhere, as long as you've got pymol in your PATH or you explicitly include the directory where the pymol executable is. If you do it in the directory where you're foo.pml file is, you can just do 'pymol foo.pml'. Otherwise you could still do 'pymol /home/hally/somedirectory/foo.pml'. The same goes if you've just started pymol. If you've started it in the correct directory, you can just do @foo.pml. In any case you can do @/home/hally/somedirectory/foo.pml. You could also, within pymol, change directories to go to the place where you have the script, as Lieven suggests. The thing is, you need to tell the computer where the programs/scripts are. It can't know it by itself. It only 'knows' which directory it was called from. Cheers, Tsjerk On 1/23/08, Hally Shaffer <gt...@ma...> wrote: > I installed pymol onto a linux system. I can open the program, open the pdb > file, and open a .pse file, but I cannot open the .pml file which contains the > manipulations that I've already made. Any suggestions? > > -- > Hally Shaffer > <>< Graduate Student > Georgia Institute of Technology > School of Chemistry and Biochemistry > gt...@ma... > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |