Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe <anas...@mbu.iisc.ernet.in> wrote:
> > Hi, > > I have been trying to use the script draw_links.py at > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links > between each pair of c-alpha atoms present in an atom selection. > Once I load a PDB (1q16.pdb) and make an atom selection, lets say : > PyMOL>select pk1, name CA in resi 5+10+15+12+16 and chain C , on the > PyMOL>command-line in pymol, I > do : PyMOL>run draw_links.py > > I wanted to visualise links between all pairs of calpha atoms present in > the atom selection, pk1. > However I am unable to do that using draw_links.py > I am doing: PyMOL> draw_links pk1 > > How can I do this using draw_links.py? > Where am I going wrong? Perhaps the instructions are not clear enough, but the script is not designed to automatically draw links between all pairs of C-alphas in a selection. It expects two different selections and it will draw links between the first residue of each selection and then the second and so on. It doesn't therefore make sense to give it the same selection for both because, in your example, it draws a zero-length link between residue 5 and residue 5, and another between residue 10 and residue 10 and so on. You will have to run the script multiple times to get the links you want: draw_links name CA & resi 5 and chain C, name CA resi 10 and chain C draw_links name CA & resi 5 and chain C, name CA resi 15 and chain C draw_links name CA & resi 5 and chain C, name CA resi 12 and chain C Sorry that it doesn't quite do what you were expecting! I designed it for the situation where I have two structures that exhibit a conformational change and I wanted to show how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ 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
