Combining volumes in the new Chimera version
Hello, I just downloaded the new Chimera version and tried to combine different models (density maps) into one volume, using the new 'combine' function, (e.g. combine #1 #2), but it returned an error message. Is it only possible to combine atomic structures (such as PDB files), or is there a way to combine volumes/density? Thanks a lot! Martin P.S.: Thank you so much for developing Chimera! I enjoy working with this program a lot! . . . . . . . . . Martin Kampmann The Rockefeller University 1230 York Avenue New York, New York 10021 USA phone: ++1 212 327 8101 fax: ++1 212 327 7880 e-mail: Martin.Kampmann@rockefeller.edu
On Dec 9, 2008, at 2:13 PM, Martin Kampmann wrote:
Hello,
I just downloaded the new Chimera version and tried to combine different models (density maps) into one volume, using the new 'combine' function, (e.g. combine #1 #2), but it returned an error message.
Is it only possible to combine atomic structures (such as PDB files), or is there a way to combine volumes/density?
Yes, "combine" can only combine molecular models. I'm not even sure how you would combine maps unless 2 out of 3 of their dimensions were the same and they were precisely aligned along the remaining axis.
Thanks a lot! Martin
P.S.: Thank you so much for developing Chimera! I enjoy working with this program a lot!
We're happy you like it! Except for "combine" of course. ;-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Martin, Chimera doesn't have a way to add maps yet. The volume operation, vop, command would be the logical place to support that. A command like "vop #0 add #1 extend true sample true multiplier 0.25" could be implemented to add two maps extending the grid of first map #0 to cover the second and sampling the second map values (since its grid points won't generally align with those of the first map's grid) and scale the second map to allow getting comparable normalizations. I'll add this to the feature request list. Tom Martin Kampmann wrote:
Hello,
I just downloaded the new Chimera version and tried to combine different models (density maps) into one volume, using the new 'combine' function, (e.g. combine #1 #2), but it returned an error message.
Is it only possible to combine atomic structures (such as PDB files), or is there a way to combine volumes/density?
Thanks a lot! Martin
P.S.: Thank you so much for developing Chimera! I enjoy working with this program a lot!
. . . . . . . . .
Martin Kampmann
The Rockefeller University 1230 York Avenue New York, New York 10021 USA
phone: ++1 212 327 8101 fax: ++1 212 327 7880 e-mail: Martin.Kampmann@rockefeller.edu
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Eric Pettersen -
Martin Kampmann -
Tom Goddard