Registration and VRML output for molecules
Julio Ortiz asks about registration behind a fire wall, and VRML output for molecules (ribbons, sticks, spheres). Tom ------- Start of forwarded message ------- Date: Wed, 09 Mar 2005 09:09:04 +0100 From: Julio Otiz <ortiz@biochem.mpg.de> To: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Registration-VRML-Chimera Hi Thomas: A couple of question: 1) Chimera registration: When I try to register from our institute, behind a firewall, I can not register, I received an error message as there were not internet connection. For my personal computer is not a problem. I can do it from home, but for other computers at the institute, it could be a problem. I would like to update all our versions from chimera, so..how to deal with the registration problem afterwards? 2) VRML export of pdb file representations: As far as I know Chimera can export surfaces of density maps to VRML format. It is possible to export some representation of a pdb files, like ribbons, sphere or sticks also to VRML?. There are some programs that do it, so maybe could be a nice feature to introduce in Chimera (if is not already possible). Greetings, Julio ------- End of forwarded message -------
I can certainly answer the first question. One of the Chimera preference categories (under Favorites) is "Web Access". In that category you can tell Chimera to use a proxy web server and designate that proxy. Doing so will allow registration to work through a firewall. I will defer to those more learned than myself on the second question. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Mar 9, 2005, at 9:23 AM, Thomas Goddard wrote:
Julio Ortiz asks about registration behind a fire wall, and VRML output for molecules (ribbons, sticks, spheres).
Tom
------- Start of forwarded message -------
Date: Wed, 09 Mar 2005 09:09:04 +0100 From: Julio Otiz <ortiz@biochem.mpg.de> To: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Registration-VRML-Chimera
Hi Thomas: A couple of question:
1) Chimera registration: When I try to register from our institute, behind a firewall, I can not register, I received an error message as there were not internet connection. For my personal computer is not a problem. I can do it from home, but for other computers at the institute, it could be a problem. I would like to update all our versions from chimera, so..how to deal with the registration problem afterwards?
2) VRML export of pdb file representations: As far as I know Chimera can export surfaces of density maps to VRML format. It is possible to export some representation of a pdb files, like ribbons, sphere or sticks also to VRML?. There are some programs that do it, so maybe could be a nice feature to introduce in Chimera (if is not already possible).
Greetings, Julio
------- End of forwarded message ------- _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Wed, 9 Mar 2005, Thomas Goddard wrote:
------- Start of forwarded message -------
Date: Wed, 09 Mar 2005 09:09:04 +0100 From: Julio Otiz <ortiz@biochem.mpg.de> To: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Registration-VRML-Chimera
A couple of question:
2) VRML export of pdb file representations: As far as I know Chimera can export surfaces of density maps to VRML format. It is possible to export some representation of a pdb files, like ribbons, sphere or sticks also to VRML?. There are some programs that do it, so maybe could be a nice feature to introduce in Chimera (if is not already possible).
So to answer the second question, there is currently an experimental X3D output option that is only available on the command line with the x3dsave command. X3D is the immediate successor to VRML. Chimera outputs the XML version of X3D, so you can use various XML translation tools to convert it to your prefered format. All of the geometry is in the X3D file. FYI, there appears to be a bug with non-flat ribbons, but everything else should work. - Greg
participants (3)
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Eric Pettersen
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Greg Couch
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Thomas Goddard