[Chimera-users] Chimera- Imod file size problems

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 2 12:30:00 PST 2013


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 <ariane.briegel at gmail.com> 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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