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

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 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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