id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6561	volume sdLevels option gives wrong levels on multiple volumes	mmaestro@…	Tom Goddard	"

Begin forwarded message:

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

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
"	defect	closed	moderate		Volume Data		fixed						all	ChimeraX