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

[Moisés Maestro López]

Thanks a lot

> El 8 abr 2022, a las 20:44, Tom Goddard <goddard at sonic.net> escribió:
> 
> Great!  Thanks for reporting the problem.  I fixed it in Chimera today too.  But I encourage everyone to use ChimeraX.  Usually we don't do fixes to Chimera anymore unless they are critical, but it only needed a few lines of code changed just like in ChimeraX so I fixed Chimera too.
> 
> 	Tom
> 
> 
>> On Apr 8, 2022, at 8:49 AM, Moisés Maestro López <mmaestro at cnb.csic.es <mailto:mmaestro at cnb.csic.es>> wrote:
>> 
>> 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 <mailto: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 <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/20220411/36f30c04/attachment.html>