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Date: Thu, 16 Feb 2006 23:47:38 -0800 From: Janet Iwasa jiwasa@gmail.com To: Thomas Goddard goddard@cgl.ucsf.edu Subject: chimera vrml issues...
Hi Tom,
I was trying out some of those new scene export functions in Chimera that you showed me a while back, and I've been running into some issues. I've got a large ribbon structure that I wanted to export as VRML, but Chimera only wrote a small file that couldn't be opened. Using notepad, all the file included was the following:
#VRML V2.0 utf8
Transform { children [ ] }
Saving as a X3d file seemed to work (seemed like a reasonable size at 10 MB) but I couldn't use the translator (X3dToVrml97.xslt) to change to VRML since it appeared to run into memory issues.
Trying to save as POV or Renderman either failed or crashed Chimera.
Any suggestions?
Janet
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Hi,
Is it possible to save the pdb file in the same format as we loaded into Chimera? This is because the MD program that I am using does not recognize Chimera format.
Any help will be appreciated.
Batsal Devkota.
Graduate Student Georgia Tech Atlanta, GA 30339
Hi Batsal, I am not sure I understand the question. You can save PDB files or Mol2 files as described in http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html
These are the only formats currently available for writing out molecular coordinates. Currently there is no way to save MD trajectories in any of the other MD formats, only as PDB (after playing all of the frames you want to save, choose File... Save PDB or one of the other methods described in the man page above and use the setting to Save "all frames").
I am not sure what you mean by "Chimera format" - there isn't really a Chimera format for molecular structure, unless you mean a session file, or perhaps a PDB file written by Chimera. Why not use the original MD format in the MD program? I am not sure why you want to put the data through Chimera before going back to the MD program.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Feb 24, 2006, at 10:03 AM, Batsal Devkota wrote:
Hi,
Is it possible to save the pdb file in the same format as we loaded into Chimera? This is because the MD program that I am using does not recognize Chimera format.
Any help will be appreciated.
Batsal Devkota.
Graduate Student Georgia Tech Atlanta, GA 30339 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Batsal Devkota -
Elaine Meng -
Thomas Goddard