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

[Enrico Martinez]

Thanks!
I've just checked, there is the same issue with the chimeraX-daily (I
am using macOSX Big Sur )

This what I see from the bash terminal

NOTE: available bundle cache has not been initialized yet

NOTE: Updating list of available bundles failed: [Errno 60] Operation timed out

executed make_muto.cxc

Otherwise ChimeraX-13 works pretty well on the same configuration!

пт, 17 июн. 2022 г. в 09:44, Greg Couch <gregc at cgl.ucsf.edu>:
>
> That check should be done asynchronously and not affect the startup
> time.  We will take a look.
>
>      -- Greg
>
> On 6/17/2022 12:42 AM, Enrico Martinez via ChimeraX-users wrote:
> > 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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