[Chimera-users] Volume blob and sum internal map value(s)

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 17 14:32:18 PST 2019

Hi Lothar,
Unfortunately not really (without coding) since “sel” is the only way of specifying the blobs individually in a command, and clicking on them is the only way to select them.  Surely it could be done with python, probably avoiding selection entirely, but somebody else would have to advise on that.  

About blob center, it is even more annoying, I’m afraid… although the center of “mass” of the masked map could be reported with “measure center”, it is given in grid indices.  If you add a marker at the center with the “mark true” option, then you can use “measure center” on the marker to get actual coordinates.  However the marker is a new model so you have to know the next available model number and probably you’d want to delete it before you create the next one.

For example

measure center #3 mark true
… if that gives marker model #4, then …
measure center #4
close #4

(I was hoping that it would work just to use command “cofr sel” which will would change the center of rotation to the selected blob and report that center in the Reply Log.  However, that gives different numbers, and when I add a new atom with those coordinates, is not in the right place… must be in a different coordinate system than the molecule and map.)

Sorry about the hassle,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 17, 2019, at 10:07 AM, Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov> wrote:
> Hi Elaine, 
>   it seems to be working. Since I have a number of peaks and a number of different maps to deal with, is there a way to iterate over all blobs in a map without having to click on them ? If iteration works, is there a way to write out the blob center in adition to its integrated value so I can match it with a nearby heavy atom (I need to know which blob stems from which atom of course) ?
> Thanks,
> Lothar
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wednesday, January 16, 2019 9:07:27 PM
> To: Esser, Lothar (NIH/NCI) [E]
> Cc: chimera-users BB
> Subject: Re: [Chimera-users] Volume blob and sum internal map value(s)
> Hi Lothar,
> It’s a little more circuitous:
> (1) use “sop split” to make the blobs independently selectable (otherwise when you select any one blob, it selects all the blobs in the same surface model)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#split>
> (2) select the blob of interest (Ctrl-click)
> (3) mask map with selected blob, e.g. for map #0 command something like: 
> mask #0 sel mod #3
> …model #3 is the new masked map
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
> (4) use “measure mapSum” on new map to sum all of its values, e.g.
> measure mapsum #3 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapSum>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jan 16, 2019, at 3:15 PM, Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov> wrote:
> > 
> > Hi, 
> >   I seem to remember that the following is possible but I cannot figure it out anymore:
> > 
> > One can read, say, an electron density map, contour it at desired level and in "Measure and Color Blobs" one can individually select blobs that are of interest and determine their volume and surface area. 
> > 
> > That works well. What I don't remember is how to integrate the map values inside the blob. I think it was implemented once but it currently escapes me. 
> > 
> > Any advice welcome. 
> > Thanks, 
> > Lothar
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