[Chimera-users] isosurface and blobs

[Raffaele Raucci]

Hi Elaine and Tom,

thank you for your replies.

I will try Tom's trick to estimate the number of isosurfaces.

Raphael (or Raffaele ;D)

2015-11-12 20:44 GMT+01:00 Tom Goddard <goddard at sonic.net>:

> You can convert a map surface to one where each connected blob is a
> separate surface piece, then measure their area and volume using the
> following commands
>
> open emdbID:1080
> sop split #0 model #5
> measure volume #5
> measure area #5
> close #5
>
> with output to the Reply Log (in Favorites menu) that looks like:
>
> emd_1080.map split ? 1:  volume = 2389
> emd_1080.map split ? 3:  volume = 73628
> emd_1080.map split ? 2:  volume = 2425.3
> emd_1080.map split ? 9:  volume = 4.008
> emd_1080.map split ? 4:  volume = 2417.6
> …
> emd_1080.map split ? 1:  area = 1403.7
> emd_1080.map split ? 3:  area = 43120
> emd_1080.map split ? 2:  area = 1431.9
> emd_1080.map split ? 9:  area = 16.329
> emd_1080.map split ? 4:  area = 1463.1
>
> The blobs are number (82 in this example), but it seems they aren’t
> printed out in order — but you can count the lines when you process this
> data to see how many blobs there are.  Volume and area are in Angstrom^3
> and Angstrom^2 if the grid spacing of the map is given in Angstroms.
>
>         Tom
>
>
> > On Nov 12, 2015, at 9:33 AM, Elaine Meng  wrote:
> >
> > Hi Raphael,
> > Sorry no, there is no command (or even GUI tool, as far as I know) to
> count the number of blobs at a given contour level.
> >
> > There is also no command to measure the area and volume of a specific
> blob.  There is only the “Measure and Color Blobs” GUI, since to specify
> each blob you have to pick it by mouseclick.
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html
> >
> >
> > Commands “measure area” and “measure volume” only measure the whole
> surface, that is, all of the blobs together.
> > Best,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >
> >> On Nov 12, 2015, at 5:54 AM, Raffaele Raucci wrote:
> >>
> >> Hi all,
> >>
> >> I imported in chimera a map file with .cube extension.
> >>
> >> I was able to show isosurface after setting specific isovalue.
> >>
> >> Can you tell me if it is possible, by command line, count the number of
> different blobs displayed as isosurface?
> >>
> >> Is it also possible determine the area and volume of each blob?
> >>
> >> Thanks in advance,
> >>
> >> Raphael
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>


-- 
Regards
Raffaele Raucci, Ph.D.
Laboratoire de Biologie Computationnelle et Quantitative
UMR 7238 CNRS/UPMC - Paris
15, rue de l' Ecole de Medicine
75006
FRANCE

raf.raucci at gmail.com
raffaele.raucci at upmc.fr

Mobile: +33 (0)752277944
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