VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Wed Jun 25 2014 - 07:55:08 CDT

Hi all

My name is Sergio and I'm trying to run a script which do a
representation after a mouse atom selection (using vmd_pick_atom
callback) is done. I can see the rep before the crash event. I suppose
I'm doing something wrong, but I can't figure it out. VMD crashes with
this error:

Package: rlwrap-0.37-1.fc14
Latest Crash: Wed 25 Jun 2014 07:07:07 AM
Command: rlwrap -C vmd -c '-b()[],&^%#;|\\\\' -f
/usr/local/lib/vmd/vmd_completion.dat
/usr/local/lib/vmd/vmd_LINUXAMD64 full_gel_for_LP.gro
Reason: Process /usr/bin/rlwrap was killed by signal 11 (SIGSEGV)
Comment: None
Bug Reports:

Here below I paste the script in order that someone can help me to
find out what is wrong with it..(Thank you very much ....!!)

proc clat { dist } {

puts "###########################################"
puts "Enable trace: write enabletrace"
puts "###########################################"
puts "press P on the screen and then"
puts "select the choline's N "

global vmd_pick_event vmd_pick_atom dist_global
set dist_global $dist

#Enable trace
proc enabletrace {} {
global vmd_pick_event vmd_pick_atom dist_global
trace variable vmd_pick_event w clatrato
}

#Disable trace
proc disabletrace {} {
global vmd_pick_event vmd_pick_atom dist_global
trace vdelete vmd_pick_event w clatrato
}

#Atom selections
proc clatrato { args } {
    global vmd_pick_event vmd_pick_atom dist_global

    set sel1 [atomselect top "{same residue as water and within
$dist_global of (index $vmd_pick_atom)}"]
    set N_chol [atomselect top "index $vmd_pick_atom"]
    set my_resi [$N_chol get resid]
    set sel2 [atomselect top "resid $my_resi"]
    puts "my_resi: $my_resi"

#adding water molecules around Choline's atoms
   mol delrep 0 top
   mol representation Licorice 0.1 10 10
   mol color Name
   mol selection "[$sel1 text]"
   mol addrep top
   mol showrep top 0 on

#adding hbonds among water molecules
   mol representation HBonds 3.5 30 2.0
   mol color ColorID 4
   mol selection "[$sel1 text]"
   mol addrep top
   mol showrep top 0 on

#adding lipid resid
   mol representation Licorice 0.2 10 10
   mol color Name
   mol selection "[$sel2 text]"
   mol addrep top
   mol showrep top 0 on

   display resetview

}
} 

-- 
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221