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

[Tom Goddard]

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> 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
> 
> 
> 
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