From: James S. <jms...@gm...> - 2011-11-01 18:26:05
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Dear Pymol Users! I want to solve one methodologycal problem via Pymol. I have 20 x-ray structures of one protein presented in different conformations. The main problem is that all those structures consist of Hen Lysozyme inserted in the protein for the improvement of the crystallographic properties of those structures. I want to load my all 20 tructures in PyMol by one command from worked dir and make alignment of that enssemble with one structure where there is no such insertion. As the consequence b this algorithm I want detect lyzocyme insertion in all my structures wich I want to deleate. How I could realize all that via PyMol console ? James |
From: Jason V. <jas...@sc...> - 2011-11-01 19:55:45
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Hi James, PyMOL can do what you want, but you need to monitor the scientific validity at each step. First load all your proteins into PyMOL. If that must happen in one command, please see LoadDir (http://pymolwiki.org/index.php/LoadDir). Next, for the target protein with no insertion, let's call it "target", select A > Align > all to this. This should align the objects to "target" and create a new object called "aln_all_to_target". Last, select/remove those atoms in the other proteins and not in the alignment: select toRemove, (not target) and (not aln_all_to_target) remove toRemove You need to ensure that the alignment object truly picked up the correct regions: do not blindly remove atoms without first inspecting them. Cheers, -- Jason On Tue, Nov 1, 2011 at 2:25 PM, James Starlight <jms...@gm...> wrote: > Dear Pymol Users! > > > I want to solve one methodologycal problem via Pymol. I have 20 x-ray > structures of one protein presented in different conformations. > The main problem is that all those structures consist of Hen Lysozyme > inserted in the protein for the improvement of the crystallographic > properties of those structures. > > > I want to load my all 20 tructures in PyMol by one command from worked dir > and make alignment of that enssemble with one structure where there is no > such insertion. As the consequence b this algorithm I want detect lyzocyme > insertion in all my structures wich I want to deleate. > > How I could realize all that via PyMol console ? > > James > > ------------------------------------------------------------------------------ > RSA® Conference 2012 > Save $700 by Nov 18 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: James S. <jms...@gm...> - 2011-11-21 16:21:25
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Jason, but as I've understood super did alignment only for two structures, Is there any way to do the same operation for ensemble ? (for CE as I understood this could be done by alignto command but it lack for seq alignment iin this case) James 2011/11/21 Jason Vertrees <jas...@sc...> > Hi James, > > > set fetch_host, pdbe > > Your PyMOL looks to be outdated. This was added to the open-source in > v1.3r1, I think. > > > By the way could you also help me with the alignment of my structure ( > I've > > posted this question today at this topic). I think that I should use the > > combination of the structure alignment ( like CEalign) with the common > seq. > > alignment but I dont know exactly how :( > > You should use the 'cealign' or 'super' commands to do this. Cealign > uses only structure, whereas 'super' uses both structure and sequence. > Please continue to post questions like this to the list for best > results: there are some very smart people on our PyMOL list. > > Cheers, > > -- Jason > > > > > James > > > > 2011/11/21 Jason Vertrees <jas...@sc...> > >> > >> James, > >> > >> > 1) I've already tried to use it but the downloading was to slow. How I > >> > can > >> > change source for pdb downloading ? E.g set fetch_host didnt worked :( > >> > >> set fetch_host, pdbe > >> > >> should work. Please let me know if it doesn't. > >> > >> > >> > 2) How I can specify individual chain for uploading via fetch command? > >> > >> You can't--PyMOL downloads the entire structure. To show just a given > >> chain type something like: > >> > >> fetch 1hpv > >> > >> # "c. A" means "chain A" > >> > >> color blue, c. A > >> > >> Use similar selectors, for example > >> > >> # remove all atoms from the structure > >> # except those in chain B > >> > >> remove not chain B > >> > >> Cheers, > >> > >> -- Jason > >> > >> > >> > >> -- > >> Jason Vertrees, PhD > >> PyMOL Product Manager > >> Schrodinger, LLC > >> > >> (e) Jas...@sc... > >> (o) +1 (603) 374-7120 > > > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: James S. <jms...@gm...> - 2011-11-22 09:11:25
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By the way also I've tried use super_all script wich can do multiple alignment via Super command pldserver1.biochem.queensu.ca/~rlc/work/*pymol*/*super_all*.py but as the consequense the resulted sequence alignment in CGO in pair-wise manner. How could I make something like this super all but for just one reference ( similar to the align ) so I'd like to obtain multiple sequence alignment on one reference based on the multiple structure alignment. Thanks James 2011/11/21 James Starlight <jms...@gm...> > Jason, > > but as I've understood super did alignment only for two structures, Is > there any way to do the same operation for ensemble ? (for CE as I > understood this could be done by alignto command but it lack for seq > alignment iin this case) > > > > James > > 2011/11/21 Jason Vertrees <jas...@sc...> > >> Hi James, >> >> > set fetch_host, pdbe >> >> Your PyMOL looks to be outdated. This was added to the open-source in >> v1.3r1, I think. >> >> > By the way could you also help me with the alignment of my structure ( >> I've >> > posted this question today at this topic). I think that I should use the >> > combination of the structure alignment ( like CEalign) with the common >> seq. >> > alignment but I dont know exactly how :( >> >> You should use the 'cealign' or 'super' commands to do this. Cealign >> uses only structure, whereas 'super' uses both structure and sequence. >> Please continue to post questions like this to the list for best >> results: there are some very smart people on our PyMOL list. >> >> Cheers, >> >> -- Jason >> >> > >> > James >> > >> > 2011/11/21 Jason Vertrees <jas...@sc...> >> >> >> >> James, >> >> >> >> > 1) I've already tried to use it but the downloading was to slow. How >> I >> >> > can >> >> > change source for pdb downloading ? E.g set fetch_host didnt worked >> :( >> >> >> >> set fetch_host, pdbe >> >> >> >> should work. Please let me know if it doesn't. >> >> >> >> >> >> > 2) How I can specify individual chain for uploading via fetch >> command? >> >> >> >> You can't--PyMOL downloads the entire structure. To show just a given >> >> chain type something like: >> >> >> >> fetch 1hpv >> >> >> >> # "c. A" means "chain A" >> >> >> >> color blue, c. A >> >> >> >> Use similar selectors, for example >> >> >> >> # remove all atoms from the structure >> >> # except those in chain B >> >> >> >> remove not chain B >> >> >> >> Cheers, >> >> >> >> -- Jason >> >> >> >> >> >> >> >> -- >> >> Jason Vertrees, PhD >> >> PyMOL Product Manager >> >> Schrodinger, LLC >> >> >> >> (e) Jas...@sc... >> >> (o) +1 (603) 374-7120 >> > >> > >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> > > |
From: Thomas H. <sp...@us...> - 2011-11-22 09:19:31
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Hi James, paste the following piece of code into the PyMOL command line. It does more or less the same as "A > align > all to this" but with "super" instead of "align". names = cmd.get_object_list() for name in names[1:]: cmd.super(name, names[0], object='aln') The first object in the list will be used as reference structure. The "aln" object which will be created represents the "all to reference" alignment. Cheers, Thomas James Starlight wrote, On 11/22/11 10:11: > By the way also I've tried use super_all script wich can do multiple > alignment via Super command > pldserver1.biochem.queensu.ca/~rlc/work/ > <http://pldserver1.biochem.queensu.ca/~rlc/work/>pymol/super_all.py > > but as the consequense the resulted sequence alignment in CGO in > pair-wise manner. How could I make something like this super all but for > just one reference ( similar to the align ) so I'd like to obtain > multiple sequence alignment on one reference based on the multiple > structure alignment. > > Thanks > > James > > 2011/11/21 James Starlight <jms...@gm... > <mailto:jms...@gm...>> > > Jason, > > but as I've understood super did alignment only for two structures, > Is there any way to do the same operation for ensemble ? (for CE as > I understood this could be done by alignto command but it lack for > seq alignment iin this case) > > > > James > > 2011/11/21 Jason Vertrees <jas...@sc... > <mailto:jas...@sc...>> > > Hi James, > > > set fetch_host, pdbe > > Your PyMOL looks to be outdated. This was added to the > open-source in > v1.3r1, I think. > > > By the way could you also help me with the alignment of my > structure ( I've > > posted this question today at this topic). I think that I > should use the > > combination of the structure alignment ( like CEalign) with > the common seq. > > alignment but I dont know exactly how :( > > You should use the 'cealign' or 'super' commands to do this. Cealign > uses only structure, whereas 'super' uses both structure and > sequence. > Please continue to post questions like this to the list for best > results: there are some very smart people on our PyMOL list. > > Cheers, > > -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |