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From: James S. <jms...@gm...> - 2012-01-26 12:45:43
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Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to make turn motif in the STG tripeptide only by changing dihedral of this amino acids. When I've tried make it by means of DYNOPLOT plugin the rest of the alpha helix was distorded. Is there any possible ways to make this conversion ? James |
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From: Thomas H. <sp...@us...> - 2012-01-26 16:27:52
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Hi James, the modeling capabilities of PyMOL are rather limited, there are probably more powerful tools for such tasks. Without guaranty that the result will be reasonable, try this: # lock all but the STG tripeptide protect not pepseq STG # activate sculpting sculpt_activate all set sculpting # switch to edit mode edit_mode Now drag atoms with the mouse or pick bonds and use commands like "torsion". Hope that helps. Cheers, Thomas James Starlight wrote, On 01/26/12 13:45: > Dear PyMol users! > > I'm looking for the possible way to change some backbone didedral values > in my peptide and dont perturbe the secondary structure of the rest of > the peptide. > > E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to > make turn motif in the STG tripeptide only by changing dihedral of this > amino acids. When I've tried make it by means of DYNOPLOT plugin the > rest of the alpha helix was distorded. > > Is there any possible ways to make this conversion ? > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
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From: Jed G. <je...@gm...> - 2012-01-26 16:33:06
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James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you require. Jed Thomas Holder wrote: > Hi James, > > the modeling capabilities of PyMOL are rather limited, there are > probably more powerful tools for such tasks. > > Without guaranty that the result will be reasonable, try this: > > # lock all but the STG tripeptide > protect not pepseq STG > > # activate sculpting > sculpt_activate all > set sculpting > > # switch to edit mode > edit_mode > > Now drag atoms with the mouse or pick bonds and use commands like "torsion". > > Hope that helps. > > Cheers, > Thomas > > James Starlight wrote, On 01/26/12 13:45: >> Dear PyMol users! >> >> I'm looking for the possible way to change some backbone didedral values >> in my peptide and dont perturbe the secondary structure of the rest of >> the peptide. >> >> E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to >> make turn motif in the STG tripeptide only by changing dihedral of this >> amino acids. When I've tried make it by means of DYNOPLOT plugin the >> rest of the alpha helix was distorded. >> >> Is there any possible ways to make this conversion ? >> >> James > |
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From: James S. <jms...@gm...> - 2012-01-27 06:23:02
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Dear Thomas, Jed! Firstly, thanks for the advise in further days I'll try Modeller software! But also I've tried to use above advises in PyMol and in general I was satisfy with the results. I have just only several questions 1- What exactly is the Sculpping ? As I've understood its something like real-time minimisation of the edited structure. Is what cases this might be better than rigid rotation\edition of the selected bonds/ angles by mouse-mode editing ? :) 2- I'm looking for the possible way to set the values for psi and phi dihedral-angles. As I understood the commands like torsion or set dihedrals need in the definition of the edited angles. Is there more trivial way to set values for the pre-defined backbone dihedrals like set phi value, sele, 120 ? :) Something like this I can do via DynoPlot plugin where I can move point on the graph wich correspond to the pair of psi-phy angles but I need in more accuracy way to define the exactly values of this dihedrals. Thanks again, James 2012/1/26 Jed Goldstone <je...@gm...> > James- > > I think you need to seriously consider using software that's actually > designed to compute and refine protein models, such as Modeller. There > are forcefield and structural constraints that PyMol is just not > designed to do, and your results may not have the scientific validity > you require. > > Jed > > Thomas Holder wrote: > > Hi James, > > > > the modeling capabilities of PyMOL are rather limited, there are > > probably more powerful tools for such tasks. > > > > Without guaranty that the result will be reasonable, try this: > > > > # lock all but the STG tripeptide > > protect not pepseq STG > > > > # activate sculpting > > sculpt_activate all > > set sculpting > > > > # switch to edit mode > > edit_mode > > > > Now drag atoms with the mouse or pick bonds and use commands like > "torsion". > > > > Hope that helps. > > > > Cheers, > > Thomas > > > > James Starlight wrote, On 01/26/12 13:45: > >> Dear PyMol users! > >> > >> I'm looking for the possible way to change some backbone didedral values > >> in my peptide and dont perturbe the secondary structure of the rest of > >> the peptide. > >> > >> E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to > >> make turn motif in the STG tripeptide only by changing dihedral of this > >> amino acids. When I've tried make it by means of DYNOPLOT plugin the > >> rest of the alpha helix was distorded. > >> > >> Is there any possible ways to make this conversion ? > >> > >> James > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: James S. <jms...@gm...> - 2012-01-27 08:54:59
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Also I've tried to test set_dihedral command but failed :) E.g I want to change PHI value ( the angle beetween H-N and C-alpha-C-beta in the residue) I've type set_dihedral resi 40 and name H, resi 40 and name N, resi 40 and name CA, resi 40 and name CB, -30 and obtain error Selection 1 doesn't contain a single atom/vertex. I suppose this error might be due to incorect definition of H atom in the first selection. By the way how I could define PHI in case if my structure lack for hydrogens at all ? James 2012/1/27 James Starlight <jms...@gm...> > Dear Thomas, Jed! > > Firstly, thanks for the advise in further days I'll try Modeller software! > > But also I've tried to use above advises in PyMol and in general I was > satisfy with the results. > > I have just only several questions > > > 1- What exactly is the Sculpping ? As I've understood its something like > real-time minimisation of the edited structure. Is what cases this might be > better than rigid rotation\edition of the selected bonds/ angles by > mouse-mode editing ? :) > > 2- I'm looking for the possible way to set the values for psi and phi > dihedral-angles. > > As I understood the commands like torsion or set dihedrals need in the > definition of the edited angles. Is there more trivial way to set values > for the pre-defined backbone dihedrals like > > set phi value, sele, 120 > > ? > :) > > Something like this I can do via DynoPlot plugin where I can move point on > the graph wich correspond to the pair of psi-phy angles but I need in more > accuracy way to define the exactly values of this dihedrals. > > > Thanks again, > > > James > > > 2012/1/26 Jed Goldstone <je...@gm...> > >> James- >> >> I think you need to seriously consider using software that's actually >> designed to compute and refine protein models, such as Modeller. There >> are forcefield and structural constraints that PyMol is just not >> designed to do, and your results may not have the scientific validity >> you require. >> >> Jed >> >> Thomas Holder wrote: >> > Hi James, >> > >> > the modeling capabilities of PyMOL are rather limited, there are >> > probably more powerful tools for such tasks. >> > >> > Without guaranty that the result will be reasonable, try this: >> > >> > # lock all but the STG tripeptide >> > protect not pepseq STG >> > >> > # activate sculpting >> > sculpt_activate all >> > set sculpting >> > >> > # switch to edit mode >> > edit_mode >> > >> > Now drag atoms with the mouse or pick bonds and use commands like >> "torsion". >> > >> > Hope that helps. >> > >> > Cheers, >> > Thomas >> > >> > James Starlight wrote, On 01/26/12 13:45: >> >> Dear PyMol users! >> >> >> >> I'm looking for the possible way to change some backbone didedral >> values >> >> in my peptide and dont perturbe the secondary structure of the rest of >> >> the peptide. >> >> >> >> E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to >> >> make turn motif in the STG tripeptide only by changing dihedral of >> this >> >> amino acids. When I've tried make it by means of DYNOPLOT plugin the >> >> rest of the alpha helix was distorded. >> >> >> >> Is there any possible ways to make this conversion ? >> >> >> >> James >> > >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > |
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From: Thomas H. <sp...@us...> - 2012-01-27 09:14:31
Attachments:
set_phipsi.py
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> 1- What exactly is the Sculpping ? As I've understood its something like > real-time minimisation of the edited structure. Is what cases this might > be better than rigid rotation\edition of the selected bonds/ angles by > mouse-mode editing ? :) It's a geometry optimizer. It has bond/angle/torsion/vdw terms as far as I can judge from the various sculpt_* settings and the "Build > Sculpting" menu. http://www.pymolwiki.org/index.php/Molecular_Sculpting http://www.mail-archive.com/pym...@li.../msg09358.html > 2- I'm looking for the possible way to set the values for psi and phi > dihedral-angles. > > As I understood the commands like torsion or set dihedrals need in the > definition of the edited angles. Is there more trivial way to set values > for the pre-defined backbone dihedrals like > > set phi value, sele, 120 see attachment. It's the function from DynoPlot, modified to work with selections. Note that you can quickly query phi/psi angles with "phi_psi" command. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
