January 2012 - Chimera-users - RBVI Mailing Lists

Regarding Bonding Pattern and all residue
by Vivek Keshri 30 Jan '12

30 Jan '12

Dear Sir / Madam, I Vivek Keshri writing from Uttar Pradesh India, I am opening docked PDB file in Chimera 1.5.3 and want to identify all residue of receptor and ligand which are involved in binding. Waiting for favorable response... Yours Sincerely, Vivek Keshri +91-8005261512

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Minimisation error
by Kyle Morris 30 Jan '12

30 Jan '12

Hi, I get a minimisation error - Atom type "Br" is not supported by MMTK - when trying to minimise a PDB that contains a bromonaphthalene covalently bound ligand. I have read the post by neelagiri.d at gmail.com and note the Cl substitution does make this work but my Br is part of the molecule and so GAFF/Antechamber should be able to handle it I thought? Really appreciate any help. Best wishes, Kyle

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Re: [Chimera-users] pythonw.exe error
by Gutheil, William 30 Jan '12

30 Jan '12

Im am getting the same error as noted in this post: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005790.html Is this a graphics problem? Any suggestions to fix? THanks

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Images
by George Tzotzos 30 Jan '12

30 Jan '12

Hi everybody, When I'm saving images either as tiff or pgn, the void around the image can ON OCCASIONS be quite large. The example attached below. Is there a way of reducing the void space? Regards George

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Chimera output into Collada .dae file format
by Evan Kantrowitz 30 Jan '12

30 Jan '12

Hi, This is the way I got it to work, I exported Chimera scene to VRML (.wrl). Next you need blender. You can download it from http://www.blender.org/download/get-blender/ Then Open Blender. In the upper right corner in the Scene section right click on Lamp and delete it right click on Cube and delete it right click on Camera and delete it Save this file so you don't have to do this every time. I called mine empty_blender_file.blend Either open empty_blender_file.blend or continue from above and read in the the .wrl file from Chimera File -> import->X3D Extensible 3D (.x3d/.wrl) this reads in the file In Blender you need to delete the three lights that came in from Chimera called TOPO, TOPO.001 and TOPO.002 In the upper right corner in the Scene section right click on TOPO and delete it right click on TOPO.001 and delete it right click on TOPO.002 and delete it Now you need to move around the viewport to get it centered In the upper right corner in the Scene section click on the Viewport then press number pad 0 Press the cube icon below the Scene section Now in the transform section move the location x,y,z. When you have it the way you want it is ready for export. File->export->collada (.dae) Done. This file will read into iBooks Author and have somewhat uniform lighting. By the way, .dae files can be opened an checked in Preview. Its easier than going back and forth into the iPad, since you can rotate the image in Preview. Here is a link to a .dae file of 1crn that you can import into iBooks Author or Preview http://dl.dropbox.com/u/4300550/1crn2_mod.dae Hope this helps, let me know if it works for you and if you have any suggestions. Finally, someone needs to write a one step VRML and/or X3D to collada converter that will work with PyMol and Chimera etc. PS It was a little easier from PyMol, if your interested see the post at https://discussions.apple.com/thread/3670156?start=0&tstart=0 PSS. Okino Computer Graphics makes a .wrl and .x3d to .dae converter http://www.okino.com Have fun! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

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Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

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Re-order models in function of their rmsd regarding a given structure
by Jean Didier Pie Marechal 27 Jan '12

27 Jan '12

Hi everyone, I have a set of protein and would like to morph between them in the smoothy manner. I'd like then, to re-order following the rmsd regarding a given structure. What would be the command-line, script that could do this relatively easily? All the best. JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Re: [Chimera-users] Morph conformation: Starting all movies in the same time
by Elaine Meng 27 Jan '12

27 Jan '12

Hi Damien, You would use the "movie" command to control the recording. That is, your script would include movie commands to start recording before the coordset command, stop recording, and then encode into movie file. Command documentation and example movie command scripts: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> I hope this helps, Elaine On Jan 27, 2012, at 5:16 AM, Damien Larivière wrote: > Dear Elaine, Tom and Eric, > > Many many many thanks for that! That's perfect! I have been able to clearly see a real difference between two of the 4 morph conformations. RMSD also indicates differences but it is more difficult to interpret. > > Great! > > I have another question: Since it is possible to display the deformation for the 4 models, can we record a movie of all the morph conformations? > > Damien > > ps: Tom, for your information, I tried coordset #0-3 1,100 but it retrurned "Must specify 1 molecule, got 4". I probably downloaded the daily build (windows 64bits) too early ? > > > On 26/01/2012 20:16, Tom Goddard wrote: >> Hi Damien, >> >> I improved the coordset command so you can say >> >> coordset #0-3 1,100 >> >> in tonight's Chimera daily builds. (Will not be in the Chimera 1.6 release candidate though.) Using multiple commands separated by semicolons or the above single command will play all trajectories in sync. >> >> Tom >> >>> On Jan 26, 2012, at 10:03 AM, Elaine Meng wrote: >>> >>>> You could try putting four coordset commands together with semicolons, e.g. something like: >>>> >>>> coordset #0 1,100; coordset #1 1,100; coordset #2 1,100; coordset #3 1,100 >>>> >>>> That should all be one line... the e-mail program may break it up. You would substitute the model numbers of your morph trajectories and frame numbers as appropriate, and you could include other "coordset" options. >>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> >>>> >>>> I'm not completely sure they would start simultaneously, but that's my best guess of what to try. >>> >>> As far as I know, they should start at the same time. If they don't, let us know! >>> >>> --Eric >>> >> >

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Trajectory analysis: RMSD
by George Tzotzos 27 Jan '12

27 Jan '12

Hi everybody, I'm wondering if there's a way to find out per-residue RMSD fluctuation in a trajectory. I'm trying to find the parts of the backbone that show the greatest RMSD fluctuation against a reference structure. A good weekend to you all George

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