VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Sat Sep 03 2011 - 14:38:17 CDT

Dear Andrea, we write this script. it can help you. ############################################################### # sasa.tcl                                                    # # DESCRIPTION:                                                # #    This script is quick and easy to provide procedure       # # for computing the Solvent Accessible Surface Area (SASA)    # # of Protein and allows Users to select regions of protein.   # #                                                             #    # EXAMPLE USAGE:                                              # #         source sasa.tcl                                     # #         Selection: chain A and resid 1                      # #                                                             # #   AUTHORS:                                                  # #    Sajad Falsafi (sajad.falsafi_at_yahoo.com)               # #       Zahra Karimi                                          #  #       3 Sep 2011                                           # ###############################################################   puts -nonewline "\n \t \t Selection: " gets stdin selmode # selection set sel [atomselect top "$selmode"] set protein [atomselect top "protein"] set n [molinfo top get numframes] set output [open "SASA_$selmode.dat" w] # sasa calculation loop for {set i 0} {$i < $n} {incr i} {     molinfo top set frame $i     set sasa [measure sasa 1.4 $protein -restrict $sel]     puts "\t \t progress: $i/$n"     puts $output "$sasa" } puts "\t \t progress: $n/$n" puts "Done."      puts "output file: SASA_$selmode.dat" close $output >________________________________ >From: David Tanner <dtanner_at_ks.uiuc.edu> >To: Andrea Holfelder <andreaholfelder_at_gmx.com> >Cc: namd-l_at_ks.uiuc.edu >Sent: Thursday, August 25, 2011 6:17 PM >Subject: Re: namd-l: SASA of PBD files > > >VMD has a command: > > >measure sasa 1.4 $atomselection > >Thank you, >David E. Tanner > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >David E. Tanner >Theoretical and Computational Biophysics Group >3159 Beckman Institute >University of Illinois at Urbana-Champaign >405 N. Mathews >Urbana, IL 61801 >http://www.linkedin.com/in/davidetanner >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > >On Sat, Aug 20, 2011 at 4:11 AM, Andrea Holfelder <andreaholfelder_at_gmx.com> wrote: > >I am looking for a simple tcl script that could calculate the sasa for range of pdb files over a loop or something. >>I googled some scripts but they seemed very complicated and had many more usages. >>A simple command that could carried out within a loop of tcl should be enough or a simple script. >> >>Andrea Holfelder >> > > >