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: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://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
