Dear Sirs, I recently started using chimera, please apologise my lack of knowledge. In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? If you know, please point out the article which describes the procedure for this kind of volume calculation. Best regards, Alex
Hi Alex, Surfnet in Chimera does not produce a volume, only surfaces. It calculates the volume but then computes surfaces and deletes the volume. If you would to measure the enclosed volume of the disconnected pieces produced by surfnet, first make those pieces independently selectable with command sop split #0 where #0 is the id for the surfnet model (use Favorites / Model Panel to find the correct id number). Then select the piece of interest (ctrl click on it), then get its enclosed volume with command measure volume sel To type commands to Chimera use menu Favorites / Command Line. This question belongs on the chimera-users mailing list, not the chimera-dev list which is for programming issues. Tom
On May 6, 2015, at 8:18 AM, Alex wrote:
Dear Sirs, I recently started using chimera, please apologise my lack of knowledge. In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? If you know, please point out the article which describes the procedure for this kind of volume calculation.
Best regards, Alex _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>
Hi Alex, The Surfnet results are just surfaces in Chimera without associated volume data. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html> That is, they are just the hollow “skins” without data values inside and outside, and Chimera “volume” tools such as Volume Eraser don’t apply. Chimera uses the term volume data for 3D grids of values, typically maps of electron density or electrostatic potential. Some other approaches for studying pocket void space are mentioned in this recent post to chimera-users@cgl.ucsf.edu: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html> I can’t think of any Chimera-only approach to intersect 3D shapes. There is volume data addition, subtraction, and masking with surfaces (see commands “vop add/subtract” and “mask”), but in that case you would need to have some volume data by Chimera’s definition. The Voss Volume Voxelator site mentioned in the post above does create volume data to fill pockets in proteins, but I don’t know if it would work with such subsequent manipulations in Chimera. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> I hope this clarifies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. the chimera-users address mentioned above is probably better for general usage questions; chimera-dev is for programming-related questions On May 6, 2015, at 8:18 AM, yes sir <fileslave@hotmail.com> wrote:
Dear Sirs, I recently started using chimera, please apologise my lack of knowledge. In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? If you know, please point out the article which describes the procedure for this kind of volume calculation.
Best regards, Alex
participants (3)
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Elaine Meng -
Tom Goddard -
yes sir