Hi, If you want to draw all bonds for all pairs between two selections, you can just use bond:
bond sele and n. ca, sele and n. ca Hope it helps, Tsjerk On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell <robert.campb...@queensu.ca> wrote: > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada ------------------------------------------------------------------------------ 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
