[Chimera-users] Fo-Fc electron density maps

Tom Goddard goddard at sonic.net
Mon Jun 30 11:00:23 PDT 2014

Hi Oliver,

  To simplify your Chimera macros a bit you can put multiple options in one volume command.  Instead of

	volume # capfaces false; volume # style mesh; volume # meshlighting false; volume # squaremesh false

you can change settings for all open maps with

	volume # capfaces false style mesh meshlighting false squaremesh false


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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