- Chimera-users - RBVI Mailing Lists

some questions about Chimera
by Ruijie Chen 02 Aug '13

02 Aug '13

Dear Sir / Madam: I am a 3D animation student who recently started to making medical animation videos, and I found Chimera is a very usefull tool for building molecules and proteins. However, there are few things that I don't understand: 1. After I import a .dae file which exported from hemoglobin (PDB: 2hhb), I found that the color I have set for each ribbon is gone, the one I have got inside maya is a hemoglobin molecule with one color. And when I want to select each alpha or beta-globin, I failed to do so because there sometimes have some polygons from other alpha or beta-globin. Is there a way to solve these problems? 2. I have tried to export the scene to a .wrl file and convert it to mayafile via wrl2ma, but when I open the finish converted maya file it always give me lots of error messages like this : "Error: file: C:/Users/**/hemo_ribbon.ma line 116: setAttr: Too much data was provided. The last 173 elements were not used. // " and this :"// Error: file: C:/Users/**/hemo_ribbon.ma line 13078: setAttr: Too much data was provided. The last 1193 elements were not used. // " Is this a problem which happen during the export process of Chimera or some other reasons? Looking forward for your reply Thank you -- With kind regards Ruijie Chen

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Re: [Chimera-users] Using Surfnet tool in a per-frame python script
by Elaine Meng 01 Aug '13

01 Aug '13

Hi William, Thanks for your kind words! I'd like to suggest an alternative approach: accumulate occupancy for the ligand over the whole trajectory and then show an isosurface for that occupancy map. You'd have to contour at a low level (e.g. 1 for everywhere the ligand has been during at least 1 frame), but in my mind at least, this produces a nice blob showing everywhere the ligand has been. I don't know how successful it would be on this specific data, but it should be relatively easy to try (no scripting involved). It may depend on how flexible everything is and how much it moves around… you can hold steady based on some set of atoms, but there may still be residual "motion blur." See the "Occupancy Analysis" section of the MD Movie man page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…> You would have to first indicate atoms to "hold steady" (if an appropriate set exists, or maybe your trajectory is already pre-processed to keep the structure in the same place and orientation as possible), select the ligand, and then in the occupancy calculation dialog choose appropriate settings. Sounds like you would turn off (set to false) "limit data collection to within cutoff…" and "collect data separately…", maybe decrease "volume grid spacing" to get a less chunky final result, and adjust anything else as you see fit. As for pruning, you can hide disconnected bits of surface using Hide Dust and/or erase parts of a volume dataset using Volume Eraser (both in menu under Tools… Volume Data). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/hide…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> Just an idea, but maybe worth a try… Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > First, thank you all for such a wonderful program! Also, thanks to the > users' list for such quick, thorough, and always-helpful answers! > > Second, a little background: I have a gromacs MD simulation (well several, > actually) of a small ligand diffusing through a protein. Because the ligand > requires the entire simulation to traverse the protein cavity, I was > thinking of using the Surfnet tool to accumulate or "build-up" the cavity > interface between the ligand and protein using a per-frame python script a > la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line > thread on this mailing list. I was thinking I could then "prune" the > accumulated SurfaceModel using the surfvol.py script available on the > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page.

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Using Surfnet tool in a per-frame python script
by William McDonald 31 Jul '13

31 Jul '13

Dear Chimera Developers, First, thank you all for such a wonderful program! Also, thanks to the users' list for such quick, thorough, and always-helpful answers! Second, a little background: I have a gromacs MD simulation (well several, actually) of a small ligand diffusing through a protein. Because the ligand requires the entire simulation to traverse the protein cavity, I was thinking of using the Surfnet tool to accumulate or "build-up" the cavity interface between the ligand and protein using a per-frame python script a la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line thread on this mailing list. I was thinking I could then "prune" the accumulated SurfaceModel using the surfvol.py script available on the http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page. Now, I can generate a Surfnet surface easily (as Eric points out) for each MD frame using the python commands from Surfnet import interface_surfnet interface_surfnet("LigandAtoms","ProteinAtoms") But how, if possible, can I combine all the individual SurfaceModels into one surface? Also, and not secondarily, does this seem like a reasonable approach to obtain the ligand-protein cavity surface? Thanks again for all your generous support. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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Hello
by A Amiri 30 Jul '13

30 Jul '13

Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.

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Amino acid scanning
by Alper Yilmaz 30 Jul '13

30 Jul '13

Hi, We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion. I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not. I'll write a demo script (more probably python script) to substitute certain amino acids with all standard amino acids and then minimize the structure. As far as I know, Chimera can not calculate free energy, so I will save the PDB files and then use another program to calculate the free energy. My first question is, whether the commands below are appropriate for my purpose or not? The sample below is a snippet from an exhaustive list. I preferred to save the information regarding clashes before the minimization just to keep record. swapaa ala :22.a findclash :22.a log true saveFile clash_report_22ala minimize nogui true write #0 test_22ala swapaa val :22.a findclash :22.a log true saveFile clash_report_22val minimize nogui true write #0 test_22val swapaa ile :22.a findclash :22.a log true saveFile clash_report_22ile minimize nogui true write #0 test_22ile ... My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each. Thanks, Assist.Prof.Dr. Alper YILMAZ Department of Bioengineering Faculty of Chemical and Metallurgical Engineering Yildiz Technical University Esenler, Istanbul/TURKEY 34210 Phone: +90.212.383-4657 (office) Fax: +90.212.383-4625

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Using Chimera in a non-graphics environment
by Devan Bicher 24 Jul '13

24 Jul '13

To Whom it may concern, Hi, my name is Devan Bicher and I am a researcher at Lehigh University. I am working on computational studies of proteins and Chimera's findHBond function is extremely useful! I have been using chimera a lot recently, however since I am working with a number of different protein/substrate combinations it would be great for me to use findHbond in a batch sort of way in which I can supply numerous inputs and allow chimera to run on all of them. Does chimera have any sort of built in batch processing option like this? -- -Devan Bicher Bioengineer, Computer Science minor Lehigh University

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volume viewer window
by jparmache＠lmb.uni-muenchen.de 24 Jul '13

24 Jul '13

Hello, I would like to ask, whether there could be a possibility to define how many density levels one is able to see at the same time in the Volume Viewer window? Currently, there are max 3, however, with larger monitors, this could be for some beneficiary if one could define the max amount. What do you think, would that be possible ? Best regards, Jean-Paul Armache

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ViewDock Data Analysis
by felipe vasquez 24 Jul '13

24 Jul '13

Hi, I have been executing a couple of docking processes through Autodock vina module in Chimera. Nevertheless, I am a bit confused about the docking analysis, because although I obtained a score for a certain number of ligand poses, I do not know if this number (-9.2, as an example) is expressed in kcal/mol, kj/mol, or even another units. On the other hand, I could not understand the meaning of RMSD l.b and RMSD u.b. What are they? and what role the play in the docking analysis procedure? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Docking with Autodock vina (Chimera)
by felipe vasquez 24 Jul '13

24 Jul '13

Hi, I am trying to perform a docking process via the tool 'autodock vina' embedded into chimera menu. However, once I am baout to run the process, I always obtain the same message: Service 'opal:vina_1.1.2' is unavailable. What can I do in order to overcome this problem? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Feature Request
by R.J. Swett 18 Jul '13

18 Jul '13

Hey there, I was wondering if you could enable movie encoding to .wmv in an upcoming build? I know ffmpeg supports that format, so hopefully it'd be an easy update. I usually have to re-encode videos, for some reason my new computer won't play most videos while using presenter-view with HDMI output. It's just a finicky little thing, but it'd make my life a lot easier. I've found a some other people with the same issue with HDMI-output only computers. -- R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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