- Chimera-users - RBVI Mailing Lists

Crash with Intel graphics on Windows fixed
by Greg Couch 12 Sep '08

12 Sep '08

We have been seeing a large number of bug reports from Windows laptops with Intel graphics (both XP and Vista, as well as desktop systems) with the lastest chimera production release, 1.2540. The symptoms include, but are not limited to, jumbled surface triangles, incorrect lighting, "unable to share data" errors, wglMakeCurrent failures, "pure virtual function called", and the inability to exit chimera. The bug has been isolated to the Intel graphics driver and a workaround has been added to chimera. The fixed version of chimera is available today in the Daily Builds section on the chimera website, <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>. Greg Couch UCSF Computer Graphics Lab

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grid across graphic
by Barry Lever 11 Sep '08

11 Sep '08

AS a new user of Chimera, I apologize for asking what , for many of you, is probably a trivial question.... initially when using Chimera ,creating an image (using pseudobond Reader) and then saving an image file, (save image) all worked well, but in the last couple of days, every time I save an image file in whatever mode (png, tif, jpg etc), I get my image with a heavy black grid across it.(and on two different computers). I am using Chimera 1.254. Is there a simple fix- it feels like a conflict. Thanks for your help (Windows XP, SP3) a low resolution example is appended Barry -- A B P Lever Distinguished Research Professor Emeritus York University, Chemistry CB124 4700 Keele St., Ontario, Canada, M3J 1P3 Tel: 416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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rotational/translational shift from reference structure
by KATRYNA CISEK 11 Sep '08

11 Sep '08

Dear Chimera developer, I would like to analyze a set of dimer structures based on a reference dimer structure. Unfortunately a simple RMSD calculation does not capture the translational/rotational shift that occurs. Is it possible to extract a plane of rotation and degree of rotation between two structures in chimera? Thanks, Katryna

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rmsd in nogui mode
by Ryan 10 Sep '08

10 Sep '08

Hi again, I'd like to save the rmsd values calculated by chimera's 'rmsd' command when running in 'nogui' mode. What's the best way to go about this? Thanks! -ryan

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addh question
by P. Law 10 Sep '08

10 Sep '08

Hi, I am analyzing water-water and water-protein hydrogen bonds in a dataset of high resolution crystal structures. As part of this analysis, I will need to add hydrogens to water molecules and to the protein. I was wondering how well the "addh" tool can place hydrogens on water molecules in the first shell around the protein? If addh is not the right tool for this task, are you aware of any freely available programs that can add hydrogens to 1st shell water molecules in PDB files? Thanks for your help! Sincerely, Peter Law Graduate Student Biochemistry Department University of Washington

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importing general 3D models into Chimera
by Jeff Triffo 09 Sep '08

09 Sep '08

hi users, I figure someone on this list has run across this before. I have been using a modeling/CAM tool - Rhino - to generate a 3D model that I would like to import into Chimera, if possible. Does anyone have a "best way" to go about doing this? Rhino is a NURBS modeler that will export as .dxf or .dwg (AutoCAD), .ai (Adobe Illustrator), .fbx (MotionBuilder), .obj (Wavefront), .igs/.iges (IGES), .sat (ACIS), and .stl (Stereolithography). It also saves in its native format - .3dm - but that is a NURBS (openNURBS) format and I realize that Chimera does not render NURBS. Of the export options above, having limited familiarity with Illustrator, I am unsure what the nature of "3D" is in that format. thanks for any suggestions, -Jeff

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surface capping command
by Gabriel Lander 09 Sep '08

09 Sep '08

Is there a way to turn on surface capping from the Chimera command line?

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saving images -- wire representation at higher dpi
by Ryan 09 Sep '08

09 Sep '08

Hi, I am trying to save higher resolution images that contain some residues with a wire width of 2. I have noticed that when i increase the dpi of the images, the saved images look different than what is displayed in the viewer -- nodes appear at each atom of the residues that are displayed as wires. As i increase the dpi of the saved images, the nodes become increasingly exaggerated (of a thicker radius than the wire bonds). Is this what should be happening? If so, is there a way to have both the atoms and bonds save with the same radius? Thanks a lot, ryan

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Models or chain
by hsosa＠aecom.yu.edu 09 Sep '08

09 Sep '08

I have created a model from several PDB files and saved it using the save PDB utility in chimera. The resulting PDB file had the different molecules separated in the PDB file with the lines MODEL 1 . . . MODEL 2 . . . MODEL 3 . . . and so on. Is it possible instead to save the PDB file as one model but using different chain names for the different molecules ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] reading in hdf5 files in chimera
by Joshua Turner 08 Sep '08

08 Sep '08

Hi, I have created a 3D hdf5 file and am having trouble displaying it in Chimera. Is there something specific chimera looks for that it needs to read in the .h5 file, to be able to display the file? Thanks, Josh

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