Hi Ashok Have you tried using Caver plugin in Pymol? It interprets and displays possible channels of solvent accessible areain a given PDB. It is much more interactive, and you can choose any one of the results it provides. There's also a standalone software available, but I'd prefer the plugin version. The plugin and all relevant instructions can be found here:
https://www.caver.cz/index.php?sid=199 CAVER - software tool for protein analysis and visualization<https://www.caver.cz/index.php?sid=199> www.caver.cz CaverDock is a software tool for rapid analysis of transport processes in proteins. It models the transportation of a ligand - a substrate, a product, an inhibitor, a co-factor or a co-solvent - from outside environment into the protein active or binding site and vice versa. Hope this was helpful. ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Ashok Nayak <ashokgocrac...@gmail.com> Sent: 23 January 2019 01:31:25 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cation-channel pore representation for solvent accessible area Hi Board Members, I need to draw the solvent accessible surface representation figure for a cation channel pore from the channel coordinates. The Hole program and the documentation is already handy to obtain the 2D-plot (pore radius vs channel coordinate) and the coloured dot surface but is limiting for a publishable figure. Here is what I did I used the HOLE programs sph_process and qpt_conv to obtain the dot surface file as mentioned in http://www.holeprogram.org/doc/index.html#_plotting_a_2d_graph_of_pore_radius_vs_channel_coordinate which I sourced onto VMD. I was unable to get rid off the dots which appear more than certain radius limit. I could not control these in sph_process either. Could anyone suggest me the standard way or fine steps to circumvent this ? Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
