[Chimera-users] imod

Dougherty, Matthew T matthewd at bcm.edu
Fri May 1 14:28:34 PDT 2015

I have recently been getting some imod segmentation files and have been noticing three problems

1) when I read the MRC and imod files I am having a scaling problem, and the datasets do not integrate.

For example, if the MRC voxel size is 31.22 31.22 31.22, and the origin index is 0 -114 0, I have to change the the voxel size to 3.122 3.122 3.122 , and the origin index to 0 0 0 so that graphics match correctly.  Since there are number of people in the data chain before it gets to me, I thought it might check to determine if this is known problem before going upstream to unknown people to figure out if they are getting the imod output settings correct.

2) The graphics performance with imod segmentation files is sluggish in chimera, not sure what it is in imod.  I assume that the format defines the vertices at the highest resolution corresponding with the MRC file.  Is there a way to improve the performance on the chimera side? I am not using contouring, just reading the file in default mode.

3) The segmentation has a lot of components, such as vesicles and microtubules, that have different colors.  Is there a way to break apart the components so they can be manipulated seperately? E.g., display/hide, change colors, translate and rotate.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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