[PyMOL] Automating pymol through PERL
Hello, I have a .txt file which has data in the following fashion: 19gs BSP A 1 1a2d PYX A 117 9rsa ADU A 125 7kme PRR J 382 1a0r ACE B 1 1a0r FAR G 72 . . . Fields: PDB ID LIGAND NAME CHAIN TO WHICH IT IS ATTACHED RESIDUE SEQUENCE NUMBER In such a way, I have data of around 19,200 unique pdb files which have one or more ligands attached to them. [PLEASE NOTE THAT there can be multiple ligands to a particular .pdb file attached at different positions ] For each .pdb file, I need to extract complete residues which fall within a radius of 4.5 Angstroms of the ligand. I am calling such zones as ZONE1.I mean residues that have any atom within 4.5 Angstroms of the ligand = zone1 Then after extracting ZONE1, I also want to extract complete residues which fall within a radius of 4.5 Angstroms of ZONE1.. I am calling these zones as ZONE2. I mean, residues that have any atom within 9.0 Angstroms of the ligand, but are not already in ZONE1 = ZONE2 I am looking for a way to automate Pymol by writing a .pml script, such that foreach pdb file, I have 2 additional files generated such that they are called as: 19gs_BSP_z1.pdb [for ZONE1] and 19gs_BSP_z2.pdb [for ZONE2], 1a2d_PYX_z1.pdb, 1a2d_PYX_z2.pdb and so on... Can this be done through PERL? Please suggest me an efficient way of achieving the desired output.. Thanks, -Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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] Automating pymol through PERL
Hi Anasuya, This sound like one of those very good reasons to have a go at Python, and leave Perl behind... Together with all the plain reasons to leave Perl behind :) First of all, check http://xkcd.com/353/ Assuming the file is called list.txt and you have all pdb files at hand (which is not strictly necessary, as PyMOl can download them for you), make a file called process.py with the following content from pymol import cmd def process_line(x): pdbid,res,chain,num = x.split() cmd.load(pdbid+.pdb) cmd.select(zone1,byres all within 4.5 of (chain %s and resn %s and resi %s)%(chain,res,num)) cmd.select(zone2,(byres all within 4.5 of zone1) and not zone1)) cmd.save(%s-%s-%s-%s-zone1.pdb%(pdbid,res,chain,num),zone1) cmd.save(%s-%s-%s-%s-zone2.pdb%(pdbid,res,chain,num),zone2) cmd.delete(pdbid) def process_all(filename): for line in open(filename): process_line(line) process_all(list.txt) #== After saving the file, do pymol -c process.py And that's it. Unless I made an error somewhere :P I haven't actually tested this. But the proper solution should lie along these lines :) Hope it helps, Tsjerk On Thu, Sep 29, 2011 at 8:58 AM, Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Hello, I have a .txt file which has data in the following fashion: 19gs BSP A 1 1a2d PYX A 117 9rsa ADU A 125 7kme PRR J 382 1a0r ACE B 1 1a0r FAR G 72 . . . Fields: PDB ID LIGAND NAME CHAIN TO WHICH IT IS ATTACHED RESIDUE SEQUENCE NUMBER In such a way, I have data of around 19,200 unique pdb files which have one or more ligands attached to them. [PLEASE NOTE THAT there can be multiple ligands to a particular .pdb file attached at different positions ] For each .pdb file, I need to extract complete residues which fall within a radius of 4.5 Angstroms of the ligand. I am calling such zones as ZONE1.I mean residues that have any atom within 4.5 Angstroms of the ligand = zone1 Then after extracting ZONE1, I also want to extract complete residues which fall within a radius of 4.5 Angstroms of ZONE1.. I am calling these zones as ZONE2. I mean, residues that have any atom within 9.0 Angstroms of the ligand, but are not already in ZONE1 = ZONE2 I am looking for a way to automate Pymol by writing a .pml script, such that foreach pdb file, I have 2 additional files generated such that they are called as: 19gs_BSP_z1.pdb [for ZONE1] and 19gs_BSP_z2.pdb [for ZONE2], 1a2d_PYX_z1.pdb, 1a2d_PYX_z2.pdb and so on... Can this be done through PERL? Please suggest me an efficient way of achieving the desired output.. Thanks, -Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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] distance bug
Hi, My pymol 1.4.1 works fine. can you try to ray trace and see if your objects are available but just not displayed on the standard screen? cheers, 2011/9/29 Andreas Förster docandr...@gmail.com Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently introduced? fetch 1ubq zoom 1ubq dist 9/cg2, 73/cd2 # output: object dist01 is created # distance of 10.2 is shown, but no dashed line # now check this out: # several repetitions of the next two lines disable dist01 enable dist01 # eventually lead to the appearance of the dashed line # but it gets better disable dist01 enable dist01 # The distance is enabled but neither number nor dashed line are visible disable dist01 enable dist01 # Now the number and the dashed line are back When dist01 is enabled but invisible, disabling 1ubq brings it back, but it disappears again when 1ubq is re-enabled. With other pdb files, the distance command doesn't work at all. It returns a distance of 0.0A to the screen that is only visible when the associated pdb object is disabled. I've observed this with pymol-py26 1.4-7 installed with fink on a MacBook running 10.6 and with pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1 Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine. Recently introduced bug? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ 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] distance bug
Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention. Cheers, -- Jason 2011/9/29 Andreas Förster docandr...@gmail.com: Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently introduced? fetch 1ubq zoom 1ubq dist 9/cg2, 73/cd2 # output: object dist01 is created # distance of 10.2 is shown, but no dashed line # now check this out: # several repetitions of the next two lines disable dist01 enable dist01 # eventually lead to the appearance of the dashed line # but it gets better disable dist01 enable dist01 # The distance is enabled but neither number nor dashed line are visible disable dist01 enable dist01 # Now the number and the dashed line are back When dist01 is enabled but invisible, disabling 1ubq brings it back, but it disappears again when 1ubq is re-enabled. With other pdb files, the distance command doesn't work at all. It returns a distance of 0.0A to the screen that is only visible when the associated pdb object is disabled. I've observed this with pymol-py26 1.4-7 installed with fink on a MacBook running 10.6 and with pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1 Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine. Recently introduced bug? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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] distance bug
Ah, indeed, the latest revision 3969 has a correctly working distance command. Thanks Jason. Andreas On 29/09/2011 3:08, Jason Vertrees wrote: Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention. Cheers, -- Jason -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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
