- Chimera-users - RBVI Mailing Lists

how to product a color scale bar
by C.J. 03 Dec '10

03 Dec '10

Dear all, I am writing to ask how to product a scale bar to indicating different radius with different color when I visualizing a spheric structure with Chimera. Thanks. Regards! C.J.

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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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Closest Waters
by Beale, John 30 Nov '10

30 Nov '10

I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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Merging mrc map
by Massimiliano MALETTA 30 Nov '10

30 Nov '10

Hello I would like to know if merging two maps is possible in Chimera. I have two *mrc map files and I would like to figure out how to get a third file containing the two maps, just summed. I tried the option morph volume, but in fact it is always down weighting one of them respect to the other. Thank you for the help. ----------------------------- Post-doc IGBMC/ FRANCE MALETTA Massimiliano Equipe/Service: KLAHOLZ TEL : +33 (0) 3 88 65 57 53 FAX : +33 (0) 3 88 65 32 01

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reset/stereo
by Dougherty, Matthew T 29 Nov '10

29 Nov '10

I had a couple questions about using the reset command. Let's say I have two keyframes (e.g., kf0,kf1) such that the stereo parameters are different between the two. 1) If I do a "savepos kf0" are the stereo parameters saved as part of the keyframe? 2) If I start at kf0 and do a "reset kf1 100", should the stereo parameters be interpolated across the 100 frames? thanks, Matt

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3D dashed lines
by M Sundaramoorthy 29 Nov '10

29 Nov '10

I like to show pseudobonds (H-bonds, metal coordinations and distances) as solid dotted or dashed lines. To draw dashed/dotted line I can choose dashed line style in the Pseduobond attributes panel. But it works only with bond style 'wire' not with 'stick'. It can essentially draws flat lines. How do I show 3D dashed/dotted lines? Some images in the tutorial do have such lines represented as dotted (spheres) lines. Another problem I have is that the Side View panel shows the image but does not show the eye (the small square) and the clipping planes (vertical lines). I am using Chimera 1.5rc in Windows Vista. Thanks Sundar

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Exporting .stl
by Dennis Kolva 25 Nov '10

25 Nov '10

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.

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