Hi James, the "within" selection operator might solve your problem.
http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators Hope that helps. Cheers, Thomas On 08 Nov 2014, at 02:26, James Starlight <jmsstarli...@gmail.com> wrote: > Dear PyMol users! > > I'm writing of some automatic script aimed on the embedding of the receptors > into the membrane consisted of the pre-equilibrated lipids as well as hole > for the protein. The main issue that some of the receptors consist of the > bulky PHE or TRP side chains on their surface which are overlap with the > lipids so MD simulation of this system is crushed although of long > minimization stage prior to it. I'll be very thankful if someone provide me > with some script for PyMol or VMD for automatic detection of these problem > (overlapped) locations and removing of the overlapped lipids detected within > some cutoff radios of the protein. > > Thanks for help, > > James -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ 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
