- Chimera-users - RBVI Mailing Lists

question
by Laura Packer 20 Nov '09

20 Nov '09

To whom it may concern: I am not sure if I am sending this inquiry to the correct e-mail address. If not, I apologize for any inconvenience. I am looking to acquire a list of atoms that are within a certain distance of a set other atoms. I have googled this question and have learned how to select these atoms: bfsdjf select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 What I would like to know is how to get a list of these results. It is not appearing in my reply log as I thought it might. Thank you for your time. Sincerely, Laura Packer packer(a)bu.edu

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how to link three EM confirmations in morph map
by Chris Arthur 19 Nov '09

19 Nov '09

I am wondering what would be the best way to link three EM maps using Morph Map? I have three sequential conformations of a protein and I would like to show a movie morphing from 1 to 2 to 3 if possible. Thanks in advance for any tips. Regards, Chris Christopher Arthur Ph.D. Staff Scientist Milligan/Unwin Lab The Scripps Research Institute carthur(a)scripps.edu 858-784-7073

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<< Versions to download >>
by Hatuey Hack 18 Nov '09

18 Nov '09

Hello, I would like to know if it is possible to put the version number of Chimera in the download or to add it to the file name. Regards and keep the good work!, Hatuey ___ Mike Ditka <http://www.brainyquote.com/quotes/authors/m/mike_ditka.html> - "If God had wanted man to play soccer, he wouldn't have given us arms."

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control of scale in STL output files
by Jonathan Schaefer 18 Nov '09

18 Nov '09

Hi- I've got a question about controlling the scale of protein models in .stl files generated by Chimera under File/Export Scene in the GUI. I'm trying to print a 3D model of two interacting proteins with a rapid prototyping machine that takes .stl files as input. The two proteins are co-crystalized and contained in one .pdb file (1nbf). I want the two proteins to be printed at the same scale so that I could fit them together like legos. Can I achieve this by getting a scale set, then showing just the first chain and exporting the data to a .stl file, followed by showing just the other chain and exporting the data to a second .stl file? I'm a novice to Chimera, so I might be missing something obvious. Any help you offer will be appreciated. Jonathan Schaefer Morgan Lab UCSF

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making a movie in Chimera
by Victor Padilla-Sanchez 18 Nov '09

18 Nov '09

Hi, my name is Victor and I would have a question about a problem that I have making movies. I record the movie in MPEG 4 format and everything seems fine but when I want to play the movie in Quicktime I obtain just a black screen playing just that. Could you help me with this problem. Thank you very much Victor

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capping surface with a VRML model
by Damien Larivière 18 Nov '09

18 Nov '09

Dear all, It is possible in Chimera to cap the clipped surface of an isosurface made with the Multiscale Model tool. However, if the isosurface is exported in VRML and then reopened in Chimera, it is no more possible to cap the clipped surface. This function (surface capping) is very interesting in particular when the scene is crowded by many proteins. Is it a way to cap VRML model? Many thanks for your help! Damien

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down arrow goes all the way to empty selection
by Eric Pettersen 17 Nov '09

17 Nov '09

> On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote: > > > (4) It is great to have the down and up arrow to narrow and broaden > > selection, would be great if a final down arrow would lead to > > clearing the selection. > > After some discussion we have decided to do this, though it won't make > it into the next release since we are already in a feature freeze / > debugging mode for that. > > --Eric This is implemented now and will be in tomorrow's daily build and the eventual 1.5 release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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residue label
by Bala subramanian 17 Nov '09

17 Nov '09

Friends, I would like to know how to use our own strings with 3D label. suppose if i give 'rlabel :3', residue 3 is labelled as LEU 3. But i want to pass a string that should replace LEU 3. Hope i am clear. I know 2D label can use a string but i wish to use string especially with 3D label. Thanks, Bala

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suggestion/stereo
by Dougherty, Matthew T. 16 Nov '09

16 Nov '09

I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands. Thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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help with raytrace
by Corey Fugate 16 Nov '09

16 Nov '09

I am trying to improve image quality using the raytrace option. The script is below - reset view_1 movie record directory /Users/fugate/Desktop pattern partA_* fformat png raytrace true wait 15 delete :.B move x 1.25 15;wait wait 15 movie stop Everything works fine without "raytrace true". I should note that I do not have the movie encode command because I want to have the individual images ( for a larger Flash project). When I compare the raytrace true images produced from the script to an image generated using the "save image" option under the File menu setting "raytrace with POV" to true. Am I missing something? Corey

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