[Chimera-users] Fo-Fc electron density maps

Oliver Clarke olibclarke at gmail.com
Mon Jun 30 11:32:29 PDT 2014


Thanks Tom and Elaine, that’s very helpful!

While we’re on the topic of macros/aliases, is there any way to refer to the model ID of an output map of a command as a variable in an alias?

For example, in the normalize_to_rms macro below, I would prefer to apply all the volume settings to just the map I am normalizing, rather than all open maps, but I can’t predict the model ID of the output map because it depends on how many maps I have open. 

This would be handy for stringing together multiple map/model manipulations in a single macro - e.g. to normalize a map to rms, generate two contours and color them appropriately, without disturbing any other open maps.

Cheers,
Oliver.

On Jun 30, 2014, at 2:00 PM, Tom Goddard <goddard at sonic.net> wrote:

> 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
> 
>  Tom
> 
> 
> 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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>> 
> 




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