[PyMOL] PyMol Connectivity Data
Dear all I am confused about the requirement of providing connectivity data in a pdb file to properly render a protein with PyMol. Right now, I am displaying a pdb file not containing any connectivity data but still the protein seems perfectly valid. My question is: how does PyMol know how to properly display structures when no connectivity is provided (i understand this usually is at the end of the file in the 'CONECT...' section. Can it determine connectivity from the atom-labels, like the residue and the atom-descriptor (e.g ATOM 5 CB VAL A 1 ...)? Related to this: I'm not a specialist in protein dynamics, but i understand, every reasonable force field (AMBER, CHARMM, ...) will require me to provide connectivity, correct? The point is, i see the protein displayed correctly in PyMol, but there is no connectivity in the PDB file. Does this mean the force field computation will also work? Thanks for a statement Martin -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ 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] PyMol Connectivity Data
Dear Martin, On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger ma@bluewin.ch wrote: I am confused about the requirement of providing connectivity data in a pdb file to properly render a protein with PyMol. Right now, I am displaying a pdb file not containing any connectivity data but still the protein seems perfectly valid. My question is: how does PyMol know how to properly display structures when no connectivity is provided (i understand this usually is at the end of the file in the 'CONECT...' section. Can it determine connectivity from the atom-labels, like the residue and the atom-descriptor (e.g ATOM 5 CB VAL A 1 ...)? Related to this: I'm not a specialist in protein dynamics, but i understand, every reasonable force field (AMBER, CHARMM, ...) will require me to provide connectivity, correct? The point is, i see the protein displayed correctly in PyMol, but there is no connectivity in the PDB file. Does this mean the force field computation will also work? PyMOL simply draws bonds where atoms are close enough (defined by the sum of their vdw radii) or where there are explicit CONECT records. CONECT records are only needed where bond lengths are longer than expected. Molecular dynamics programs require explicit topology (bond lengths, angles, dihedral angles, chirality), because they are doing much more than simply making pretty pictures. So no, a force field computation will not work simply because PyMOL can draw the bonds you expect to see. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ 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] Fetch Command
Greetings, Fetch has been fixed and the code checked into SVN with some other changes. I'm calling this v1.3r1 because 'fetch' is so integral to PyMOL. For Incentive PyMOL subscribers, the new v1.3r1 builds will be available before the weekend. As usual please report any problems. Cheers, -- Jason On Wed, Aug 4, 2010 at 12:33 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Daphna, The PDB servers underwent some reorganization and moved the files on us! I will post a fix for this by tomorrow night. Thanks! -- Jason On Sun, Aug 1, 2010 at 3:44 AM, Daphna Meroz daphname...@gmail.com wrote: Dear Sir/Madam, I am using MacPymol version 1.2r1. For some reason, the fetch pdb command does not work anymore (the error message is unable to load pdb). Is there some way to resolve this? Thank you, Daphna Meroz -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ 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
