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
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 <raf.raucci@gmail.com> 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
Pardon me, that should be “Raffaele” not “Raphael” — sorry for the wrong spelling! Elaine
On Nov 12, 2015, at 9:33 AM, Elaine Meng <meng@cgl.ucsf.edu> 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 <raf.raucci@gmail.com> 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
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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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/pickblob...
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@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@gmail.com raffaele.raucci@upmc.fr Mobile: +33 (0)752277944
participants (3)
-
Elaine Meng -
Raffaele Raucci -
Tom Goddard