Re: [PyMOL] Mutagenesis script
Hi Rozaimi, the only problem seems to be your last line, you save two objects (test, 1shr) to the same PDB file. Try this: cmd.save(kill.pdb, test) Cheers, Thomas On 09/06/2011 03:25 PM, Rozaimi Razali wrote: Dear All, Sorry for the late reply and thank you for helping me out. Originally the wild residue (for 1shr) at position 36:B is a Proline. I want to mutate it to Histidine. I have tried the suggestion in this thread but the output file (kill.pdb) still gives PRO at position 36:B #Initialize fetch 1shr, async=0 create test, 1shr cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # Mutate cmd.get_wizard().set_mode(HIS) cmd.get_wizard().do_select(/test//B/36) cmd.frame(1) cmd.get_wizard().apply() cmd.set_wizard(done) # Save cmd.save(kill.pdb) I am not sure what is the problem here. I have also tried running the script on other machines and still the same problem is happening. FYI i am using Pymol version 1.3. Could this be the problem? I have tried using the log function + mutagenesis wizard in Pymol GUI but something strange is happening. The position 36:B did changed to His but e.g. input file - 1shr.pdb - atom number for 36:B:CA is 1334 output file - kill.pdb - atom number 36:B:CA 1380 log.pml - ...byresi((1shr`1380))... Why does it tag the atom number from the output file? Shouldn't it tag the atom number from the input file (1shr)? -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] Mutagenesis script
On 09/06/2011 03:43 PM, Thomas Holder wrote: Try this: cmd.save(kill.pdb, test) sorry, forgot quotes, must be: cmd.save(kill.pdb, test) -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] Mutagenesis script
So. cmd.(something) ALWAYS has to be in string format. So there is the cmd.frame wrong. Then you dont quit the mutagenesis wizard And you have a space in the cmd.save *It total, try:* #Initialize fetch 1shr, async=0 create test, 1shr cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # Mutate cmd.get_wizard().set_mode(HIS) cmd.get_wizard().do_select(/test//B/36) cmd.frame(1) cmd.get_wizard().apply() cmd.set_wizard(done) # Save cmd.save(kill.pdb) or look at: http://www.pymolwiki.org/index.php/Rotkit import rotkit *mutate test, chain=B, resi=36, target=HIS, mutframe=1* 2011/9/2 Rozaimi Razali rozaimiraz...@gmail.com Can someone please explain to me why my script is not working properly? #Initialize fetch 1shr, async=0 create test, 1shr cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # Mutate cmd.get_wizard().set_mode(HIS) cmd.get_wizard().do_select(/test//B/36) cmd.frame(1) cmd.get_wizard().apply() # Save cmd.save (kill.pdb) Thanks! -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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 -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev___ 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] Mutagenesis script
Hi Troels, cmd.(something) ALWAYS has to be in string format. So there is the cmd.frame wrong. I'm sorry but this is not true, of course you can pass an integer to cmd.frame Then you dont quit the mutagenesis wizard which is not a problem as well. And you have a space in the cmd.save I agree to avoid spaces between function name and parenthesis, but still this is valid python syntax and works fine. The full script posted by Rozaimi works fine for me by the way. cmd.set_wizard(done) this doesn't quit the wizard, cmd.set_wizard() without arguments does. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] Mutagenesis script
Dear Rozaimi, I'm sure people would bother to read your script and reply to your question if you told us what your trying to achieve and what not working properly looks like. Otherwise your wasting your time. Andreas On 02/09/2011 4:58, Rozaimi Razali wrote: Can someone please explain to me why my script is not working properly? #Initialize fetch 1shr, async=0 create test, 1shr cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # Mutate cmd.get_wizard().set_mode(HIS) cmd.get_wizard().do_select(/test//B/36) cmd.frame(1) cmd.get_wizard().apply() # Save cmd.save (kill.pdb) Thanks! -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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 -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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
[PyMOL] Mutagenesis script
Can someone please explain to me why my script is not working properly? #Initialize fetch 1shr, async=0 create test, 1shr cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # Mutate cmd.get_wizard().set_mode(HIS) cmd.get_wizard().do_select(/test//B/36) cmd.frame(1) cmd.get_wizard().apply() # Save cmd.save (kill.pdb) Thanks! -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev___ 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
[PyMOL] Mutagenesis Script with different rotamer Library!
Hi all, I'd like to use the Mutagenesis wizard in a Pymol/Python script! I'd like to automate the following steps! (1) Load a peptide pdb file with three residues. (easy) (2) Mutate one residue, well actually I do not want to change a single residue but change the rotamer of a residue. Unlike the mutagenesis wizard I'd like to use my own rotamer Library (It is based on Dunbrack's library but with slightly variations). So, I'd like to specify residue,phi,psi,chi1,chi2,chi3,chi4 for each rotamer I want to mutate to. (3) Save it in a pdb format (easy) I've found a magnificent start-up for my script from Andreas Henschel (see below). But I do not know how to load a specific rotamer (res,phi,psi,chi1,chi2,chi3 and chi4). Any ideas? All ideas are welcome, Josep Maria, PS: Well, a solution was done by the Rotamer Toggle (http://www.pymolwiki.org/index.php/Rotamer_Toggle), but this script is not working properly and out of date! - Josep Maria Campanera Alsina Juan de la Cierva Researcher Departament de Fisicoquímica Facultat de Farmàcia Avgda Joan XXIII, s/n 08028 Barcelona · Catalonia · Spain Tel: +34 93 4035988 Fax: +34 93 4035987 campan...@ub.edu -- Hi Martin, you can get hints about how to script wizard functions if you log your activities while running the wizard. A python script (mutate.py) that makes use of the mutagenesis wizard could look like this: ## run through pymol, eg.: ## pymol -qc mutate.py 1god A/94/ ASN from pymol import cmd import sys pdb, selection, mutant = sys.argv[-3:] cmd.wizard(mutagenesis) cmd.fetch(pdb) cmd.refresh_wizard() cmd.get_wizard().do_select(selection) cmd.get_wizard().set_mode(mutant) cmd.get_wizard().apply() cmd.set_wizard() cmd.save(%s_m.pdb % pdb, pdb) This is pretty no-frills, as no rotamer stuff is taken into account. I wrote it in Python, because it allows to parameterize from command line, you can add loops easily etc. Beware, the error message you get is because pymol unsuccessfully tries to open the command line arguments as files. Hope that helps. Best regards, Andreas Martin Höfling wrote: Hi there, does anybody of you has an idea, if the mutagenesis stuff is available for use inside scripts too? I wanna load a pdb, mutate a resid and save the resulting pdb via commandline. The only thing I found was modifying atoms, when I searched via help and also checked the wiki, i hope that I didn't miss sth. Cheers Martin
Re: [PyMOL] mutagenesis script
Hi Martin, you can get hints about how to script wizard functions if you log your activities while running the wizard. A python script (mutate.py) that makes use of the mutagenesis wizard could look like this: ## run through pymol, eg.: ## pymol -qc mutate.py 1god A/94/ ASN from pymol import cmd import sys pdb, selection, mutant = sys.argv[-3:] cmd.wizard(mutagenesis) cmd.fetch(pdb) cmd.refresh_wizard() cmd.get_wizard().do_select(selection) cmd.get_wizard().set_mode(mutant) cmd.get_wizard().apply() cmd.set_wizard() cmd.save(%s_m.pdb % pdb, pdb) This is pretty no-frills, as no rotamer stuff is taken into account. I wrote it in Python, because it allows to parameterize from command line, you can add loops easily etc. Beware, the error message you get is because pymol unsuccessfully tries to open the command line arguments as files. Hope that helps. Best regards, Andreas Martin Höfling wrote: Hi there, does anybody of you has an idea, if the mutagenesis stuff is available for use inside scripts too? I wanna load a pdb, mutate a resid and save the resulting pdb via commandline. The only thing I found was modifying atoms, when I searched via help and also checked the wiki, i hope that I didn't miss sth. Cheers Martin - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de
[PyMOL] mutagenesis script
Hi there, does anybody of you has an idea, if the mutagenesis stuff is available for use inside scripts too? I wanna load a pdb, mutate a resid and save the resulting pdb via commandline. The only thing I found was modifying atoms, when I searched via help and also checked the wiki, i hope that I didn't miss sth. Cheers Martin
