Re: [Chimera-users] Regarding adding plane surfaces....
On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote:
Hi Elaine,
I have three objects in the chimera image. All these objects are in different planes. How to add surfaces to each of these so that they can be shown to lie in diff planes? I have attached a typical image herewith.
Regards, Chinmaya
Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes> Please send Chimera questions to chimera-users@cgl.ucsf.edu instead of directly to me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Chinmaya, You can use the "shape rectangle" command to make planes. In the attached image I made the two planes with shape rect width 100 height 100 slab .1 color .7,.7,.7,.2 center 0,0,-50 coord #0 shape rect width 100 height 100 slab .1 color .7,.7,.7,.2 center 0,0,50 coord #0 Since I wanted the planes aligned with volume #0 I specified the "coord #0" option. Tom
On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote:
Hi Elaine,
I have three objects in the chimera image. All these objects are in different planes. How to add surfaces to each of these so that they can be shown to lie in diff planes? I have attached a typical image herewith.
Regards, Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms.
The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes>
Please send Chimera questions to chimera-users@cgl.ucsf.edu instead of directly to me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
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participants (2)
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Elaine Meng -
Tom Goddard