Hi Jeff, try this:
# given a ligand within a protein binding pocket select ligand, resn HEM # detect nearest neighbors within X distance select neighbors, polymer within 5.0 of ligand # select the residue of each neighbor, add a label label byca neighbors, resn + resi + chain # set an appropriate clipping plane zoom neighbors # shade the rest of the molecular as solid or something otherwise non # hostile to viewing. as lines show sticks, neighbors ligand show labels Hope that helps. Cheers, Thomas Jeff Johns wrote, On 06/09/12 10:51: > I am sure this has been asked many times before but I can't find the > answer after much searching... > > Is there a pymol script that, given a ligand within a protein binding > pocket, will detect nearest neighbors within X distance (not necessarily > H bonded), select the residue of each neighbor, add a label, set an > appropriate clipping plane, then shade the rest of the molecular as > solid or something otherwise non hostile to viewing. > > Something like ligplot but in 3-D. > > Many thanks, > > Dr Jeff Johns > Melatonin Research Group > Faculty of Pharmaceutical Sciences > Khon Kaen University > Khon Kaen 40002 > Thailand > Phone: +66 (0)43 202 378 > Email: jj...@kku.ac.th > Alternative email: jeffjohn...@hotmail.com -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
