Greetings, Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex. Any help in out to output the VRML file for the printer?> Thanks Andy -- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231 -------------------------------------------------
Dear Dr. Byrd, You can save the surfaces from Multiscale Models as VRML using File... Export Scene in Chimera. VRML is one of the choices (not everything in Chimera can be exported as VRML, but surfaces can). Here is the man page corresponding to our last production release (November, version 1.2184): http://www.cgl.ucsf.edu/chimera/1.2184/docs/UsersGuide/export.html Besides symmetrical multimers, Multiscale Models can also be used to generate a low-resolution surface for PDB structures that don't have any particular higher-order symmetry: a simple monomer, or something with many chains like a ribosomal subunit. Just open the structure in Chimera, start Multiscale Models (Tools... Higher-Order Structure... Multiscale Models), and then click Make Models. Multiscale Models man page: http://www.cgl.ucsf.edu/chimera/1.2184/docs/ContributedSoftware/ multiscale/framemulti.html If you run into any difficulties, please feel free to write back! Best, 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
Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex.
Any help in out to output the VRML file for the printer?>
Thanks Andy
-- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231
Just to follow up, if you export your data in the X3D format, there is a publicly available converter to convert it to VRML as documented in the Chimera User's manual (click Help in the Export Scene dialog or use the link given by Elaine and look at the paragraph about XSL). That would get you everything (surfaces, spheres, sticks, lines, and points) in VRML. We plan to make this easier someday. Greg Couch UCSF Computer Graphics Lab gregc@cgl.ucsf.edu On Tue, 17 Jan 2006, Elaine Meng wrote:
Date: Tue, 17 Jan 2006 10:17:53 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: R. Andrew Byrd <rabyrd@ncifcrf.gov> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving a multiscale model in VRML
Dear Dr. Byrd, You can save the surfaces from Multiscale Models as VRML using File... Export Scene in Chimera. VRML is one of the choices (not everything in Chimera can be exported as VRML, but surfaces can). Here is the man page corresponding to our last production release (November, version 1.2184):
http://www.cgl.ucsf.edu/chimera/1.2184/docs/UsersGuide/export.html
Besides symmetrical multimers, Multiscale Models can also be used to generate a low-resolution surface for PDB structures that don't have any particular higher-order symmetry: a simple monomer, or something with many chains like a ribosomal subunit. Just open the structure in Chimera, start Multiscale Models (Tools... Higher-Order Structure... Multiscale Models), and then click Make Models. Multiscale Models man page:
http://www.cgl.ucsf.edu/chimera/1.2184/docs/ContributedSoftware/ multiscale/framemulti.html
If you run into any difficulties, please feel free to write back! Best, 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
Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex.
Any help in out to output the VRML file for the printer?>
Thanks Andy
-- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231
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participants (3)
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Elaine Meng -
Greg Couch -
R. Andrew Byrd