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

[Enrico Martinez]

p.s. just one question regarding chimera-x 14
I've noticed that the start-up is very slow compared to the previous
version (takes 2-3 minutes both from terminal or from the application
menu with the following lag reason):

Startup Messages
notes available bundle cache has not been initialized yet
Updating list of available bundles failed: [Errno 60] Operation timed out

how may I desablel this updating list?
Thanks in advance!

пт, 17 июн. 2022 г. в 09:23, Enrico Martinez <jmsstarlight at gmail.com>:
>
> 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
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> >