[chimerax-users] Rescaling IMOD segmentation models in ChimeraX

[Tom Goddard]

Hi Matt,

  I added the "surface transform" command to ChimeraX that can scale a surface, for example,

	surface transform #1 scale 1.5 center 0,0,0

This will be in tomorrow's ChimeraX daily builds (not in ChimeraX 1.4).  I still would suggest fixing your problem in the file with IMOD.  If you use this scale operation in ChimeraX it will scale about a center point, and it could be tricky get the surface to align with your other data if the center point of the scaling is not right.

	Tom


> On Jun 2, 2022, at 7:20 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Matt,
> 
>   ChimeraX does not have any way to scale the size of a surface model such as an IMOD segmentation.  It could be hacked with a bit of Python opened in ChimeraX.  But it is usually best to have your data files encode the proper scaling in their header so I would suggest fixing it in IMOD.
> 
>   Our older program Chimera has an "sop transform" command that can scale surfaces
> 
> 	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#transform <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#transform>
> 
> Maybe I could port that to ChimeraX.  I agree it is sometimes useful.
> 
> 	Tom
> 
> 
>> On Jun 2, 2022, at 12:47 PM, Martinez, Matthew via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> Hi everyone,
>> 
>> I have a question regarding the rescaling of data in ChimeraX. I'm depicting a subtomogram average at their aligned positions in a tomogram, which doesn't contain scaled pixel information, and I want to also load in IMOD segmentation data to depict with the subtomogram average. I'm able to readjust the pixel size of the tomogram easily with the Map Coordinates dialog box, but is there a way to rescale IMOD segmentation models once in ChimeraX? I can do this within IMOD, but it would be more convenient to do it in ChimeraX with the volume. Thanks in advance for any help!
>> 
>> Best regards,
>> Matt
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