Re: [PyMOL] Connectivity
Hi Laurie, The list of bonds is accessible with cmd.get_model(), see https://pymolwiki.org/index.php/Get_Model PyMOL> m = cmd.get_model() PyMOL> print m.bond[0].index [0, 1] PyMOL> print m.bond[0].order 1 Cheers, Thomas On 26 Jan 2017, at 13:50, Laurence Williams wrote: > Dear pymol users, > > I understand that pymol does not explicitly need connectivity data to > visualise molecules as bonds are drawn when two atoms are within in a given > distance. However, once those bonds are drawn for the molecule, is > connectivity data stored somewhere whilst the file is in use? I ask with the > aim to extract that data into a python object. > > Thanks > Laurie -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] Connectivity
Dear pymol users, I understand that pymol does not explicitly need connectivity data to visualise molecules as bonds are drawn when two atoms are within in a given distance. However, once those bonds are drawn for the molecule, is connectivity data stored somewhere whilst the file is in use? I ask with the aim to extract that data into a python object. Thanks Laurie Sent from my iPad -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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
Hallo Thanks for the answer. So could PyMol generate the connectivity it sees? So this could be used for a subsequent force field computation? -- 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
Re: [PyMOL] PyMol Connectivity Data
Dear Martin, On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger 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 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
[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
[PyMOL] Connectivity Problem for Visualizing Pseudo-structure
I am using Pymol to visualize a "pseudo polymer" generated by some brownian dynamics code. We take the coordinate files generated by our simulation and convert them into a PDB file using the hetatm representation and having explicit connections defined with conect. For example: HETATM1P UNK A 2.637 1.188 0.470 HETATM2C UNK A 2.883 0.865 0.178 HETATM3N UNK A 3.176 0.740 0.564 . . . . CONECT12 CONECT2134 CONECT32 I also have the associated HETNAM and FORMUL header lines, but this doesn't seem to make any difference. Pymol displays the individual files in the trajectory fine, but when we go to load in a trajectory of structures to view as a movie, the connectivity gets weird after only a couple of frames. Random atoms are attached to each other. Another strange behavior is that after 72 frames of the movie it regains the correct bonding for one frame and then dies again. For long trajectories, in other word, frames 1,2,74, 146, 218, etc are ok. However there are only 61 atoms in each file, so I don't see an obvious reason for this cycle. If anyone wants a zipped archive of some of the pdb files to play around with, please email me. Any suggestions would be most appreciated. Joshua Adelman -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://www.ocf.berkeley.edu/~jadelman Berkeley, CA 94720 USA jadel...@ocf.berkeley.edu --
