From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 30 2014 - 22:35:40 CDT

Hi,
  Try commenting out the "hbonds" rep and see if you still have
the problem. There was a bug in the hbonds rep in some versions
of VMD that could cause a crash.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 25, 2014 at 09:55:08AM -0300, Alberto Sergio Garay wrote:
> 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
>
>

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/