in the most recent version of PyMOL, which can render measurement objects with shaders, you can also use the distance command to get a similar result:
set use_shaders set dash_gap, 0 distance sele and n. CA, sele and n. CA Cheers, Thomas On Feb 21, 2013, at 10:11 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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 -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ 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
