[chimerax-users] ChimeraX: chashes in no-gui execution

[Enrico Martinez]

i've just check, I am using chimeraX 1.3, so..
the error message can be seen directly in the bash terminal it is
something like segmentation fault and then the command associated with
the execution of the chimerax with the script

чт, 16 июн. 2022 г. в 19:35, Eric Pettersen <pett at cgl.ucsf.edu>:
>
> Hi Enrico,
>         A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish.  Your script has no ongoing motions and therefore the wait commands should do nothing.  I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes.  Are you using the 1.4 release?  What kind of error messages or output do you get when these crashes occur?
>
> --Eric
>
>         Eric Pettersen
>         UCSF Computer Graphics Lab
>
>
> > On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Dear ChimeraX users!
> > I noticed that sometimes ChimeraX crashes while being executed in
> > batch mode using bash script.
> >
> > Here is an example of my script that calculates hbonds and contacts
> > between protein and ligand
> >
> > open mypdb.pdb
> > #calculate h-bonds and contacts in each frame
> > hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false
> > interModel false makePseudobonds false log true distSlop 0.5 angleSlop
> > 20 intraRes false saveFile hbondsALL_rep1.log
> > clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff
> > 0.3 interModel false makePseudobonds false log true intraRes false
> > saveFile contactsALL_rep1.log
> > wait
> > wait
> > exit
> >
> > as you may see I added two times wait in the end of the script that
> > could reduce the frequency of crashes. May you specify what is the
> > default value for each wait (in seconds??) and how I could use just
> > one wait command to set up the pause in the proper way?
> > Many thanks in advance!
> > Cheers
> > Enrico
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at cgl.ucsf.edu
> > Manage subscription:
> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>