[Chimera-users] Segment according to fitted model

Pintilie, Grigore Dimitrie pintilie at bcm.edu
Thu Feb 25 10:01:50 PST 2016


On Feb 25, 2016, at 12:21 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi David,
If generating separate maps based on a distance cutoff from the atoms is acceptable, you could try using Color Zone (Tools… Volume Data… Color Zone).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

First you’d have to color the components different colors, then select all their atoms.  In Color Zone, use the slider to pick a suitable cutoff (if any) and then click “Split Map”  to get separate  maps for the zones.

If the components are all separate models, you could color them uniquely and then select them with commands such as:
rainbow models
select

Alternatively, although the Segment Map tool (in same menu as Color Zone) uses the watershed method and not the atoms, you could try Segment Map and then interactively group/ungroup the resulting segments to correspond with your docked components.  I don’t know how easy or hard that might be.


There is an automated way of doing this as well which isn’t hard... You can see the ‘Segmenting with Fitted Models’ tutorial here as a guide:

http://ncmi.bcm.edu/ncmi/software/segger/docs


Greg




<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>

I hope this helps,
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 Feb 25, 2016, at 8:33 AM, David Haselbach <dhaselb at gwdg.de<mailto:dhaselb at gwdg.de>> wrote:

Hi,
I do have a cryo EM map of a large complex and I fitted/modeled the individual protein components. Now I would like to segment my map according to those fitted models. Is there a possibility of doing that automatically?
Cheers
David


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