December 2010 - Chimera-users - RBVI Mailing Lists

unable to show disulfide bonds
by Mahlawat, Pardeep 02 Dec '10

02 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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display angle label
by Gesa Volkers 02 Dec '10

02 Dec '10

Dear all, I measured an angle (or better torsion) between four atoms. How can I display the angle with a label? I only found how to diplay measured distances with a label, but not angles/torsions. Thanks in advance, Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Re: [Chimera-users] Exporting .stl
by Greg Couch 01 Dec '10

01 Dec '10

Forgot to reply to list as well. -------- Original Message -------- Subject: Re: [Chimera-users] Exporting .stl Date: Tue, 30 Nov 2010 13:33:23 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Dennis Kolva <dk429(a)cornell.edu> On 11/25/2010 06:29 PM, Dennis Kolva wrote: > I have been using Chimera to export .stl files of proteins and RNA for 3D printing. The surface models print OK, but sticks or ribbons choke the printer. I looked close at the output meshes, and they have many extra surfaces which should be removed to make "legal" .stl format. > > Is that portion of the code open source? I'd like to take a closer look and see if it's possible to fix. It would be much easier to rectify the bad surfaces upon creation, rather than trying to remove them by post-processing. > > Thanks, > > Dennis Kolva > Cornell U. Presumably , you don't have a Z-Corp printer and their ZPrint software, otherwise you would output VRML from chimera and have ZPrint do the proper conversion to STL. So yes, the source code is available at http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/apps/x3d2/stl, and we would welcome improvements. I believe that the problem is that chimera does not output manifold geometry and that the X3D to STL converter would need to perform CSG operations on all of the geometry, especially the spheres and cylinders, to eliminate interpenetrating surfaces. Another issue to consider is what to do about ribbons and cylinders that are too thin for the printer you're using. Feel free to contact me directly with questions about the code or use the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu, Greg

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pythonw.exe error
by Hunmin JUNG 01 Dec '10

01 Dec '10

Hi, Whenever I open the chimera after the installation, it gives me an error 'pythonw.exe has stopped working'. It didn't matter the version of the chimera. Please what I need to do to resolve the problem. Thanks, Hunmin (Mike) Jung Department of Chemistry Texas A&M University (979)862-7639

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Chimera-users December 2010