[chimerax-users] Setting the same sdLevel threshold for several volumes

[Moisés Maestro López]

Hi Tom, 

Thanks for the response. I have downloaded the daily build and now it works. 
As far as I know the problem also happens in chimera (that is why I had to use my script). 

Best regards

Moisés

> El 7 abr 2022, a las 21:17, Tom Goddard <goddard at sonic.net> escribió:
> 
> Hi Moisés,
> 
>   That is a bug in ChimeraX.  It will be fixed in tomorrow's ChimeraX daily build.  Both of the following should work
> 
> 	volume all sdLevel 2
> 	volume #1-3 sdLevel 3
> 
> but the code processed each volume in turn and due to a bug remembered some of the level parameters from the previous volume.
> 
>   Thanks for reporting the problem!
> 
> 	Tom
> 
> 
>> On Apr 7, 2022, at 2:03 AM, Moisés Maestro López via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> Good morning, 
>> 
>> I would like to set the threshold of multiple CryoEM Volumes (10-20) at the same time, and I would like to put all of them at the same sdlevel.
>> 
>> I use the command:
>> 
>> volume #1 sdLevel 2
>> 
>> But this only work for one volume, if I use 
>> 
>> volume all sdLevel 2, or volume #1 #2 #3 sdLevel 2
>> 
>> It does not work and the threshold are random. 
>> 
>> In chimera I had a script that I use for doing that but I have not found the way to do it in ChimeraX. In Chimera, I normally called the script with an alias. 
>> 
>> 
>> 
>> alias ^allsd runscript ~/chimeraScriptSD.py
>> 
>> allsd 3
>> 
>> And the script (chimeraScriptSD.py) was:
>> 
>> import sys
>> import chimera  
>> from VolumeViewer import Volume
>> 
>> mlist = chimera.openModels.list(modelTypes=[Volume])
>> 
>> sdlevel = 2
>> 
>> if len(sys.argv)>1:
>>     sdlevel = sys.argv[1] 
>> 
>> for m in mlist:
>> 	
>> 	chimera.runCommand('volume '+str(m)+' sdlevel '+ str(sdlevel))
>> 
>> 
>> But I do not know how to do this in ChimeraX. The key point I do not know how to do is to do a loop that say “for any volume in all the opened volumes”.
>> 
>> Thanks for your help
>> 
>> Moisés
>> 
>> 
>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220408/d76682f8/attachment.html>