[Chimera-users] Chimera- Imod file size problems

Tom Goddard goddard at sonic.net
Mon Dec 2 14:12:29 PST 2013

Hi Ariane,

  Might be a bug in the Chimera IMOD mesh file reader.  When Chimera reads an IMOD mesh file it prints to the Chimera Reply Log (menu Favorites) the "pixel size" and x,y,z scale factors it found in the IMOD file.  What does it say for your file?  Can you check these parameters in IMOD?  (I don't know how to do that in IMOD.)  Seems like the problem is that z-scale is probably one, but to match your molecule it needs to be much larger.  Your images show the x and y sizes of the mesh match the molecule, but not the z size.

  You could submit a Chimera bug report (menu Help / Report a Bug…).  I would need the IMOD mesh file in order to understand what went wrong.


On Dec 2, 2013, at 12:30 PM, Elaine Meng wrote:

> Hi Ariane,
> I only know how to do it for "volume data" like MRC files and other density maps, but not for IMOD segmentation mesh  (You said "imod mrc" but then it sounded like you meant a segmentation file instead.)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod.html>
> If it's a density map, you can adjust voxel size in the Volume Viewer (choose Features… Coordinates to show those settings)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
> The same thing can also be done with the volume command, see "dimension and scale options":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
> Unless data are private, please send Chimera questions to chimera-users at cgl.ucsf.edu instead of only to me.  Then If I don't know the answer or am away from work, others can respond.
> Thanks,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 2, 2013, at 10:45 AM, Ariane Briegel < wrote:
>> Dear Elaine, 
>> I have a question you might have a quick answer to. I am trying to open a model file I generated with the IMOD program. 
>> Generally, when I open Imod mrc files in chimera the pixel size is correct in both programs. With this model the size is way off in chimera (I have never used an imod model in chimera before, just mrc files so far).
>> See screenshots below- the first one shows that the model has the correct pixel size when opened in IMOD, the second shows the wrong size in chimera (the blue and green layers should have the same height as the crystal structures below), and the last screenshot shows how the data opened in chimera (as a mesh). Is there a way for me to manually adjust the pixel size of a mesh?
>> If you have any idea how I can fix this issue I would be very grateful!
>> Thank you!
>> Ariane
>> <Screen Shot 2013-12-02 at 10.03.41 AM.png><Screen Shot 2013-12-02 at 10.35.06 AM.png><Screen Shot 2013-12-02 at 10.39.27 AM.png>
>> ––––––––––––––––––––––––––––
>> Ariane Briegel, Ph.D.
>> California Institute of Technology
>> Broad Center, MC 114-96
>> 1200 E. California Blvd.
>> Pasadena, CA 91125
>> Tel: 626-395-8848
>> Fax: 626-395-5730
>> ––––––––––––––––––––––––––––
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