[Chimera-users] query about splitting volumes using local resolution criterion

[Tom Goddard]

Hi Nilesh,

  I think what you want is the Chimera “Values at Atom Positions” tool.  It can assign to every atom the map resolution at that atom and then you use "Render by Attribute” tool to color the atoms by resolution, or you could set their transparency and then copy those colors and transparencies to the map with the Color Zone tool.  If you colored atoms for a range of resolutions the same color, then used color zone, you can then split the map according to the colors using the Color Zone split map tool.

	https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html

	https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html

	https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

	http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#descriptors <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#descriptors>

  Tom




> On May 14, 2018, at 11:29 AM, Banavali, Nilesh K (HEALTH)  wrote:
> 
> ResMap, a program that calculates local resolutions for cryoEM maps, also provides a chimera script to visualize the local resolution. This script opens Volume #0 (cryoEM map), and colors its regions using the values from Volume #1 (ResMap-generated file) as follows:
> 
> open #0 example_map.mrc
> open #1 example_map_resmap.mrc
> volume #1 hide
> scolor #0 volume #1 cmap 3.00,blue:5.00,cyan:7.00,green:9.00,yellow:11.00,orange:13.00,red
> 
> I was wondering if there is a way to generate split maps based on the resolutions stored in Volume #1 instead of just coloring the original map. Alternatively, is there way to play with the transparency of the regions with specific resolutions stored in Volume #1. The goal is to separate low resolution regions from the higher resolution regions in the original map to be able to better understand/annotate the accuracy of atomic models that are generated based on the map. 
> 
> I tried to look for ways to do this using 'volume', 'scolor zone', and 'vop' options, but was unable to make any progress. Any help would be greatly appreciated.
> 
> Thanks,
> 
> Nilesh
> 
> 
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