volume sdLevels option gives wrong levels on multiple volumes

[mmaestro@…]

Begin forwarded message:

From: Moisés Maestro López via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Setting the same sdLevel threshold for several volumes
Date: April 7, 2022 at 2:03:01 AM PDT
To: chimerax-users@…

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

[Tom Goddard]

Fixed.

The sdLevel and rmsLevel options of the volume command code modified the option values as it processed each volume resulting in this bug. Made it not modify the option values.