[Chimera-users] Fo-Fc electron density maps

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 30 09:46:55 PDT 2014

Hi Oliver and Egor,
Even if using commands, it's not necessary to split the data into two maps; analogous to the GUI approach, you can simply show two contour levels on the same data set.

For example:

volume #1 level 2.0 color green level -2.0 color red

(where you would adjust the levels to something reasonable for your data, and #1 would be whatever model is your volume data set)
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 28, 2014, at 3:14 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Dear Egor,
> In addition to Elaine’s suggestion of unchecking “Cap high values at box faces", I use the following aliases to make difference maps more familiar in style to a crystallographer:
> First, to just normalize the map to RMS (as per coot etc) and adjust to get a mesh, turn capping, mesh lighting off etc:
> alias normalize_to_rms vop scale $1 rms 1; close $1; volume # capfaces false; sop cap off; volume # style mesh; volume # meshlighting false; volume # square mesh false
> Second, to split the map into two maps (one positive, one negative), which can then be colored green and red respectively:
> alias split_diff_map vop threshold $1 minimum 0; vop threshold $1 maximum 0; close $1; sop cap off; volume # style mesh; volume # meshlighting false; volume # squaremesh false;
> I add these two lines in a “chimera_aliases.com” file, which you can  tell Chimera to read at startup under Favorites—>Preferences—>Command Line.
> You can then run these commands from the chimera command line, e.g. normalize_to_rms #1 or split_diff_map #1 if your map number is 1. Then just adjust the contours and colors in the volume viewer and you are good to go.
> I don’t know how to automatically color the resultant maps, because there does not seem an obvious way to predict their model numbers, but I am sure there is a way to do that too, perhaps via some python trickery.
> This is all kind of a work around of course - there may be a way to color a map by density value (such that all positive regions are green, and all negate regions are red), but I couldn’t figure out how to do it.
> Best,
> Oliver.

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