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

[Eric Pettersen]

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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