I'd like to convert PDB to VMRL and OBJ (for some reason hydrophobicity exports well as obj and ribbon as wrl, other than those file formats, I usually get file errors from Blender?) using Chimera via command-line call (doing them one by one will be a pain for several thousand pdb files!). How would I do this? Would I need to modify the Chimera source? (if necessary, I can do this, but it seems like it'd be pretty time consuming) Thank you guys!!! -- Calem Bendell Computer Science Dept McGill University Immunology and Microbiology Dept McGill University 438 881 9189
Hi Calem, Chimera has an "export" command, see: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> Note the OBJ export only includes surfaces. The Chimera programmer's guide has some explanation of how to loop over multiple files: <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> First you would try entering commands directly into the Command Line to figure out what commands you want to use on each structure. Then you would imbed those commands in a looping script. 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 Aug 9, 2012, at 7:19 PM, Calem Bendell wrote:
I’d like to convert PDB to VMRL and OBJ (for some reason hydrophobicity exports well as obj and ribbon as wrl, other than those file formats, I usually get file errors from Blender?) using Chimera via command-line call (doing them one by one will be a pain for several thousand pdb files!).
How would I do this? Would I need to modify the Chimera source? (if necessary, I can do this, but it seems like it’d be pretty time consuming)
Thank you guys!!!
-- Calem Bendell Computer Science Dept McGill University Immunology and Microbiology Dept McGill University
438 881 9189 _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Thanks! Also, interesting bug (possibly bug): the obj file exports are rotated 180 as compared to the wrl files. -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, August 10, 2012 1:10 PM To: Calem Bendell Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] Want to Convert PDB to VMRL? Hi Calem, Chimera has an "export" command, see: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> Note the OBJ export only includes surfaces. The Chimera programmer's guide has some explanation of how to loop over multiple files: <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> First you would try entering commands directly into the Command Line to figure out what commands you want to use on each structure. Then you would imbed those commands in a looping script. 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 Aug 9, 2012, at 7:19 PM, Calem Bendell wrote:
I'd like to convert PDB to VMRL and OBJ (for some reason hydrophobicity exports well as obj and ribbon as wrl, other than those file formats, I usually get file errors from Blender?) using Chimera via command-line call (doing them one by one will be a pain for several thousand pdb files!).
How would I do this? Would I need to modify the Chimera source? (if necessary, I can do this, but it seems like it'd be pretty time consuming)
Thank you guys!!!
-- Calem Bendell Computer Science Dept McGill University Immunology and Microbiology Dept McGill University
438 881 9189 _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
I suspect the OBJ export outputs the model in the local coordinate system of the model while the VRML export gives you the global coordinate frame which includes any interactive rotations you did. That is a bug. The OBJ code should use global coordinates so you can orient the model as you desire for the output. Tom
Thanks!
Also, interesting bug (possibly bug): the obj file exports are rotated 180 as compared to the wrl files.
-----Original Message----- From: Elaine Meng Sent: Friday, August 10, 2012 1:10 PM To: Calem Bendell Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] Want to Convert PDB to VMRL?
Hi Calem, Chimera has an "export" command, see: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>
Note the OBJ export only includes surfaces.
The Chimera programmer's guide has some explanation of how to loop over multiple files: <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
First you would try entering commands directly into the Command Line to figure out what commands you want to use on each structure. Then you would imbed those commands in a looping script. 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 Aug 9, 2012, at 7:19 PM, Calem Bendell wrote:
I'd like to convert PDB to VMRL and OBJ (for some reason hydrophobicity exports well as obj and ribbon as wrl, other than those file formats, I usually get file errors from Blender?) using Chimera via command-line call (doing them one by one will be a pain for several thousand pdb files!).
How would I do this? Would I need to modify the Chimera source? (if necessary, I can do this, but it seems like it'd be pretty time consuming)
Thank you guys!!!
-- Calem Bendell Computer Science Dept McGill University Immunology and Microbiology Dept McGill University
438 881 9189 _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (3)
-
Calem Bendell -
Elaine Meng -
Tom Goddard