[PyMOL] loadDir script
Dear PyMol users! I've forced with the problem of the loading of the my structural ensemble (pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into pymol via loadDir.pml script. In particular after loading of my ensemble in the right contex pymol's window I want to preserve structural order according to the pdb's names ( so that structures were listed in order from 1 to the 100.pdbs but not in the random (mixed) order). What additions to the loadDir script should I do to make such ordering ? James -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loadDir script
Hi James, Assuming your going from the pymol wiki loadDir script; you'd need to change glob(c) loop (sort the list in your preferred order before the loop, rather than using the result list unmodified). If I'm understanding your problem correctly (numbered pdb files being loaded as 1.pdb, 100.pdb, 2.pdb ... instead of 1.pdb, 2.pdb, ... 100.pdb) it might be easier rename your pdb files so that the default string sorting from glob matches the numerical order you want. Using the same example, the filenames would change to 001.pdb, 002.pdb, ... 100.pdb. Pete James Starlight wrote: Dear PyMol users! I've forced with the problem of the loading of the my structural ensemble (pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into pymol via loadDir.pml script. In particular after loading of my ensemble in the right contex pymol's window I want to preserve structural order according to the pdb's names ( so that structures were listed in order from 1 to the 100.pdbs but not in the random (mixed) order). What additions to the loadDir script should I do to make such ordering ? James -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loadDir script
Hi James, please try, after loading the files: PyMOL order *, yes Cheers, Thomas James Starlight wrote, On 04/02/13 19:28: Pete, thanks for suggestion. I've tried to use loadDir with the pdb's subset where each file had name like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still wrong :( also is loadDir script I found block for c in glob( g ): cmd.load(c) if ( group != None ): cmd.group( group, basename(c).split(.)[0], add ) what should I change here to sort files correctly? James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loadDir script
Thank you! Does it possible to include order *, yes to some pymol's setting file that the ordering be automatically each time when I load pdb ensemble? (I dont what to include it to the loadDir.pml script itself). James 2013/4/2 Thomas Holder thomas.hol...@schrodinger.com Hi James, please try, after loading the files: PyMOL order *, yes Cheers, Thomas James Starlight wrote, On 04/02/13 19:28: Pete, thanks for suggestion. I've tried to use loadDir with the pdb's subset where each file had name like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still wrong :( also is loadDir script I found block for c in glob( g ): cmd.load(c) if ( group != None ): cmd.group( group, basename(c).split(.)[0], add ) what should I change here to sort files correctly? James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
