Re: [PyMOL] Editing of the pdb structure
Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? James -- Try before you buy = See our experts in action! 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-dev2___ 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] Editing of the pdb structure
On 01/27/2012 09:11 AM, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! 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-dev2 ___ 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] Editing of the pdb structure
Arne, Thomas Thanks alot. Bond works finw I'd like just to ask what about geometry optimisation of the new structure E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other. When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms. How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ? James 2012/1/27 Thomas Holder spel...@users.sourceforge.net On 01/27/2012 09:11 AM, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.**php/Bondhttp://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! 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-dev2___ 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] Set values for dihedral angles
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 jmsstarli...@gmail.com 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 jedg...@gmail.com 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 x-S-T-G-xI 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 (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 -- Try before you buy = See our experts in action! 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-dev2___ 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] Editing of the pdb structure
Dear James, As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other real simulation/modelling package otherwise your results are very weak... My opinion only. João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 27 de Janeiro de 2012 09:50, James Starlight jmsstarli...@gmail.comescreveu: Arne, Thomas Thanks alot. Bond works finw I'd like just to ask what about geometry optimisation of the new structure E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other. When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms. How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ? James 2012/1/27 Thomas Holder spel...@users.sourceforge.net On 01/27/2012 09:11 AM, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.**php/Bondhttp://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! 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-dev2 ___ 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 -- Try before you buy = See our experts in action! 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-dev2___ 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] Set values for dihedral angles
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/pymol-users@lists.sourceforge.net/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 set_phipsi.py Description: application/chimera -- Try before you buy = See our experts in action! 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-dev2___ 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] single pymol installation, multiple OSes
I have a weird problem: we have a cluster of Linux computers (managed by Sun Grid Engine) running at least three different distributions of Fedora. I compiled PyMOL on the head node (Fedora 8) and I want to invoke it on the command line to generate images as part of some other computations. I'm using a custom Python installation for this, but I immediately ran into problems with another library, GLEW: File /net/chevy/raid1/nat/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/pymol/__init__.py, line 184, in module import pymol File /net/chevy/raid1/nat/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/pymol/__init__.py, line 472, in module import _cmd ImportError: libGLEW.so.1.4: cannot open shared object file: No such file or directory libGLEW.so.1.4 is what Fedora 8 has, but some of the other systems have libGLEW.so.1.5 or libGLEW.so.1.6. I also noticed that libglut has slightly different names depending on OS, but I'm not sure yet if this is going to cause problems. Has anyone dealt with this before? Is there an easy way around the problem, or do I need to install my own builds of GLEW and GLUT and link to those instead? (And if so, what do I need to do when running setup.py to get it to recognize the custom installations of these libraries?) thanks, Nat -- Try before you buy = See our experts in action! 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-dev2 ___ 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
