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

Esser, Lothar (NIH/NCI) [E] esserlo at mail.nih.gov
Thu Jan 17 10:07:37 PST 2019

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) ?



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)

(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

(4) use “measure mapSum” on new map to sum all of its values, e.g.

measure mapsum #3


I hope this helps,
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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