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

[Greg Couch]

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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