- 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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running chimera 1.8 needs root privilege
by Robert Wohlhueter 16 Jul '13

16 Jul '13

I've been using Chimera 1.5.3 under Linux (Ubuntu 12.04, 64-bit) without problems; that version I had installedas root, andis owned by root. Just now I updated to version 1.8, which, initially, I also installed as root. But trying to run it (as non-root) gave me fairly opaque error messages(copied below). On a hunch that it was a matter of privilege, I tried running with `sudo` -- which works fine. Since it was not obvious where the problem lay, I cleaned out the installation, and installed anew as a normal user (me). Accordingly, the whole installation directory tree is owned by me. But still I cannot run it (same errors) as me, but only with `sudo`. Same user, same start directory, apparently the same Python (2.7) as works with v. 1.5.3. I'm totally flummoxed! Can't imagine where the privilege hang-up is. Any hints where I should look? Thanks, Bob Wohlhueter *****************************C-shell output******************* chimera X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 198 () Serial number of failed request: 2813 Currentserial number in output stream: 2813

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Fitting multiple atomic structures in a density map
by Anindito Sen 16 Jul '13

16 Jul '13

Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position. How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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molmap and origin index
by Catalin Buiu 15 Jul '13

15 Jul '13

Hello all, I have the following problem: when I use molmap to generate a map from an atomic structure, the result is fine: both align. When I use another (Matlab) program to generate the map, the two, when opened in Chimera do not align anymore. My question is how molmap generates an origin index such that both the map and the structure do align and how Chimera reads (and converts) the xyz origin data from the MRC file? Thank you. Catalin Buiu University of Bucharest, Romania

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Euler angles in "Transform coordinates" tool
by Dan Cohen 15 Jul '13

15 Jul '13

Hello all, I have been wrecking my mind in trying to use the "Transform coordinates" tool to apply a rotation to a PDB file based on Euler angles taken from IMP. I focused my problem to the following : According to IMP, they use the ZXZ notation in the original (lab) coordinate system. According to my understanding of the chimera docs, you use ZXZ in the self (rotating) coordinate system. I have been trying to convert between those two using a python library I found on the net but keep on getting results that either show I'm missing something or a bug in somewhere. (It's called transformations.py by Christoph Gohlke) Are you aware of any issues or similar problems? I saw somewhere that someone mentioned a similar problem that was due to PDB header file with weird axis origin, but i wasn't able to get any more info. Will be thankful for any hint, Dany

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cutting the surface
by Victor Muñoz 15 Jul '13

15 Jul '13

Dear all, I want to make an image using the Surface Cliping option in Chimera. The problem is that I just want to cut the surface and not the molecule when using the Viewer to do that. As an example, I want to so something like this image from the wikipedia (http://en.wikipedia.org/wiki/File:MM_PEF.png ). Thanks for everything in advance. Kind Regards, Victor Muñoz --

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command line for silhouette representation
by Jean Didier Pie Marechal 15 Jul '13

15 Jul '13

Dear all, I am making a movie using a command file. I would like to represent the atom using the same kind of picture than those generated using the Presets option silhouette. Can you tell me how to do so? Cheers, JD Dr. Jean-Didier Maréchal Associate Professor 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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Deleting Psubobonds/Connectivity
by Dylan J. Bennett 11 Jul '13

11 Jul '13

Hi, I was wondering if there was a way to delete psudobonds and connectivity in Chimera. I use a protein-protein docking software that does not renumber chains, this results in a structure that has 2 chain As for example. When I go to analyze this in Chimera, it automatically creates a psudobond between the two chains with the same ID. Since it thinks they're connected, I can't rename the chain IDs for just one of them. I know I can hide all the psubobonds, but this doesn't really help as I still need some of them and would like to rename the chain IDs uniquely. Thank you. -- -*Dylan J. Bennett* *Dylan.John.Bennett(a)Gmail.com (914) 621-1149* *Stony Brook University* *dylan.bennett(a)stonybrook.edu* *New York Medical College* *Biochemistry* * BSB Room 102* * dylan_bennett(a)NYMC.edu*

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How Chimera reads a dcd file
by Syeda Hira Batool 10 Jul '13

10 Jul '13

Hello! I have psf and dcd files.I want to read them using my own script(non-commercial/educational purpose).So I want to know how Chimera reads dcd files.Can you please help me out in this regard by providing me some helping material or a script. Thank you Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN

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Software Chemistry Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for Your attention. Best Regards, Giovanni Ortosecco Dr. Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy Posted by: Ubuntu 13.04 Raring Ringtail http://www.ubuntu.com/about/ Use free software!

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Software Chemistry for Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for your attention. Best Regards, Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy

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color by height
by p.j.depablo 08 Jul '13

08 Jul '13

Hi everybody I am interested in coloring an EM volume by height. In this option you can change the origin and the axis of coloring. Specifically, I rotate t the structure untill a desired orientation. Then, I would like to choose the axis of coloring to be the same as the view axis, but can not find the viewing axis coordinates. Is there possible to find this informaton anywhere? Thank you in adavance. Pedro

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camera horizontal field of view
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

The camera settings allow for a horizontal field of view of 1-179 degrees. Wikipedia states that human horizontal field of view is ~180 degree. using 179 is not anything I normally recognize, looks like star trek enterprise going to warp. In cinematography books, lenses are sometimes referenced at around 20 degrees. For chimera I have found 10-30 gives nominal viewing on LCD. Setting it 1 is effectively orthographic. For DTI in a dome projection (as opposed to dome camera), I frequently will use 80-110, unless I am looking for a orthographic look, then lower values. For the mono & DTI cameras on a flat display, what are the values or the process to determine the values, for the most accurate mapping to normal human vision? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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ergonomics
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

a few suggestions on placement 1) on viewing dialog, change the location of "view all" from the sideview window, relocating it to the bottom next to reset/restore/etc buttons. having additional orthogonal buttons (x,y,z) would be avoid having to do a lot of text commands. 2) on the volume viewer dialog, saving dialog preferences is accessed through its pulldown menu; having it act like other dialogs would be helpful (ie, at the bottom like viewing dialog). 3) the main 3d graphics window when dominant , causes the default pulldown menus to appear such as when chimera starts up. when accessing volume viewing, the overall chimera pulldown menus change. The only way to get the original/main pulldown to return is to put the mouse on the 3d graphics window and doing a left click twice. Since the volume viewing has its own pulldown menus, getting this overall switch of pulldown menus eliminated would help avoid a lot of unneeded mouse movements, particularly for the situation when two displays are used, one dedicated to 3D graphics, and the other having the viz controls. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Creating Average Structure from PSF/DCD --> Include metal ions in final structure
by Peter Murphy 08 Jul '13

08 Jul '13

Hi, I am trying to create an average structure in chimera 1.7 using the built in MDtools (loading a PSF/DCD file to get the trajectory). I am able to create an averaged structure for a select number of frames easily, but it doesn't appear that the metal ions are included when the averaging occurs. Is there someway to force the ions to be included? or alternatively, is there a script to create an average structure that includes selected atoms? Thanks, Peter -- Peter Murphy, Ph.D. Candidate Department of Biochemistry and Molecular Biology Dalhousie University Halifax, NS Canada

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icosehedron enhancement
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

for the mesh adjustment, it would be good to be able to enter the radius of the mesh tubes. currently I have to select the item, go to the inspector to set the radius. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [Chimera-users] [chimera-dev] Trouble with Saving New Atom Attributes
by Elaine Meng 05 Jul '13

05 Jul '13

Hi Juliette, PDB format does not include atom-type information, as you have seen. The only sure way to save your atom type changes is to save the Chimera session. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> However: Chimera applies chemical perception to try to figure out the atom types when a structure is read in from a file. The Mol2 format does have some atom-type information, but the SYBYL Mol2 types are not related 1-to-1 to the types in Chimera. You could try saving in Mol2 format and reading it back in to see if the information you want is retained. Further, if you have added all hydrogens before writing the file (PDB or Mol2) the chemical perception is more well-determined and it is possible that it will assign the types you intended. If those do not work, however, the session is the way to go. If you just wanted a list of the assignments rather than the assignments per se, you could use "File... Save Attributes" from the menu of Render by Attribute (itself in menu under Tools... Depiction). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html…> This seems more like a "user" question than a developer (programmer) one; it's not necessary to email both lists. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 5, 2013, at 2:34 PM, Juliette Cao wrote: > Hi All, > I was successfully able to change a few atom types using the setattr command. > I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) > I saved the .pdb file > When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. > Is there a specific way to save files after using setattr command? > Regards, > Juliette Cao > University of Houston

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Trouble with Saving New Atom Attributes
by Juliette Cao 05 Jul '13

05 Jul '13

Hi All, I was successfully able to change a few atom types using the setattr command. I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) I saved the .pdb file When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. Is there a specific way to save files after using setattr command? Regards, Juliette Cao University of Houston

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force field for G-quadruplexes
by Gilmar Salgado 05 Jul '13

05 Jul '13

Hello, recently I was looking into the capabilities of Chimera minimization tools to minimize the structure of a DNA G-quadruplex molecule. The problem is that all G-quadruplexes have an ion (K+ or Na+) in-between and stabilizing the tetrads. I wonder if the force field available in chimera are "decent" to water-minimize this kind of structures? ...and which one is more adapted, after all those are non-conventional DNA structures. Thanks in advance for your input Gilmar Salgado Université Segalen Laboratoire ARNA (INSERM U869) Institut Européen de Chimie et Biologie 2 rue Robert Escarpit 33 076 Pessac Cedex FRANCE +33(0) 540 0022 24 +33(0) 557 571 015 (fax)

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Drawing with BILD commands directly from Chimera command line
by Dan Cohen 03 Jul '13

03 Jul '13

Hello all, Is there an option to type in BILD commands directly into the Chimera command line? (I know you can create a file with BILD commands and open it with Chimera but it would be helpful just to open the command line and type them in) Thank you, Dany

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Faraday Discussion on Molecular Simulation and Visualization - call for abstracts deadline 22 July 2013
by baaden＠smplinux.de 30 Jun '13

30 Jun '13

Dear Colleague, You may be interested in the following event: Faraday Discussion #169 - Molecular Simulations and Visualization ** CALL for ABSTRACTS deadline 22.7.2013 ** http://www.rsc.org/ConferencesAndEvents/RSCConferences/FD/FD169/cfp.asp A few more details: Current biology, chemistry and materials science make extensive use of computational methods ranging from applications at the cellular level, e.g. in systems biology, to detailed atomistic simulations of molecular assemblies, materials or small molecules. Faraday Discussion 169 will illustrate and discuss the potential of Human-Computer Interaction and Virtual Reality for computational molecular sciences, focusing on the following themes: * virtual and augmented reality; immersive molecular simulations * advanced visualization and visual analytics * computing power revolution and new algorithms: GP-GPUs, clouds and more * applications and serious games: from docking to protein folding Take part in the excellent scientific programme at this Discussion, in which experts in biology, chemistry and computational science will stimulate discussions and initiate research aimed at deeper involvement, beyond the boundaries of each discipline. Professor Helmut Grubmuller, Max Planck Institute for Biophysical Chemistry, Germany Dr Graham Johnson, University of California, San Francisco, USA Dr David Glowacki, University of Bristol, UK Professor Valerie Daggett, University of Washington, USA Professor Thomas Ertl, University of Stuttgart, Germany Professor Vijay Pande, Stanford University, USA Professor John Stone, University of Illinois at Urbana-Champaign, USA Dr Melanie Stegman, Federation of American Scientists, USA Assistant Professor Jim Zheng, Medical University of South Carolina, USA Professor Frederick Brooks, University of North Carolina at Chapel Hill, USA Professor Thomas DeFanti, University of California, San Diego, USA Virtual Reality represents a formidable communication and learning tool that could significantly speed up understanding of dynamic behaviour of complex biomolecular systems. This meeting is an excellent opportunity to bring the relevant disciplines closer together and benefit from collaborations across diverse fields. Yours sincerely, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

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water display problem
by inhee park 28 Jun '13

28 Jun '13

Is there a xyz coordinate range limit or a residue numbering limit in Chmiera for display? I tried to display all atoms in the PDB file using chimera version 1.8. As shown in the attached figure, not all waters were displayed. If I loaded the same PDB file using other programs such as vmd or maestro, all waters were correctly displayed. FYI, I also attached the PDB file. Thank you for your help. _________ inhee park

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Monitoring hbonds in chimera
by Neha Gandhi 28 Jun '13

28 Jun '13

Dear Users, I am trying to use hbond command in the movie tool of Chimera 1.8. I want to repeat hbond analyses with different criteria simultaneously in a single script these are my commands select :9@O1P,O2P,O3P,N,H :12@N,H findhbond selRestrictboth linewidth 2 color green reveal true (..I want to monitor hydrogen bond between these two residues with default criteria) ~sel select :3@O1P,O2P,O3P :6@O1P,O2P findhbond selRestrict any color black reveal true relax true distSlop 2.7 intraRes false ~sel When I tried these commands in one single script, I could see hydrogen bonds displayed for residue 3 and 6 and not between residues 9 and 12. Hopefully you can correct me. Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] Chimera 1.8rc 64-bit as Default Application
by Antoine Maillard 28 Jun '13

28 Jun '13

Suggestion to Dylan Bennett / Chimera 1.8rc 64-bit as Default Application Hi Dylan, you asked how to get Windows 7 to acknowledge Chimera as the default program to open specific files. In my experience the same problem was solved by running Ccleaner up to 3 times in a row to fix registry keys. After the first run, re-scanning the registry with Ccleaner shows that .pdb entries still need to be fixed. I kept running Ccleaner on my computer's registry until it was deemed as clean and only then was file association successful. Hope this helps, Antoine

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Both chimera (x86) and chimera (x86-64) fail to run on Windows 8
by David Konerding 27 Jun '13

27 Jun '13

Hi, I have a Windows 8 pro machine, 64-bit 8 GB RAM Core i3 and Quadro FX 570. When I start Chimera (x86 and x86-64), I see the splash screen then it says "pythonw.exe has stopped working". When I add --debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics I managed to cause windows to try to send an error report, which captured these files: C:\Users\dek\AppData\Local\Temp\WERF405.tmp.appcompat.txt C:\Users\dek\AppData\Local\Temp\WERF464.tmp.mdmp if those are useful for debugging, I can provide them.

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Chimera 1.8rc 64-bit as Default Application
by Dylan J. Bennett 26 Jun '13

26 Jun '13

Hi, I am attempting to associate pdb and mol2 file types with Chimera 1.8rc in Windows 7. I have tried to set it using the right-click>open with... option in Windows as well as through the control panel. I select the chimera executable, but it does not seem to accept it as a valid program, and it returns to the previous screen without adding Chimera to the box for selection. I know this is not a Windows issue, as I can set other programs and it works fine. As well, I can set other programs for the mol2 and pdb file types. Is this a known issue, is there any work around. It's not the biggest deal, but it would make my life a little easier if I could do this. It used to work in the past, but just not with the latest version. Thank you and have a great day! -- -Dylan J. Bennett Dylan.John.Bennett(a)Gmail.com (914) 621-1149 Stony Brook University dylan.bennett(a)stonybrook.edu New York Medical College Biochemistry BSB Room 102 dylan_bennett(a)NYMC.edu

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Leap Motion
by Aurélien Grosdidier 24 Jun '13

24 Jun '13

Hi all, We're planning to try Chimera with the leap motion device (https://www.leapmotion.com/) Has anyone already succeeded to do so ? Best, Aurélien.

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modeling multimers
by Francesco Pietra 24 Jun '13

24 Jun '13

Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Chimera-users Digest, Vol 122, Issue 25
by Boaz Shaanan 23 Jun '13

23 Jun '13

Hi Francesco, I doubt that modeller knows how to take into account inter-subunit information. I would be surprised if it does. As far as I know, it's a sequence-homology based model building module which also uses fold recognition and probably other pieces of information but not about oligomeric arrangement. When I dealt with a similar problem (modelling a dimer) I modelled the subunit and then superimposed each of the two subunits on top of the corresponding subunit of the known dimer, followed by Chimera's matchmaker. The resulting dimer is still considered a hypothetical structure by me. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Sunday, June 23, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 122, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. modeling multimers (Francesco Pietra) 2. Fwd: modeling multimers (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Jun 2013 07:17:44 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] modeling multimers Message-ID: <CAEv0nmt6Sy2MJcs=xk18qMGs2d5h0QOS_i7YXAJ1AEwpdWWsCQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Antw: Re: atomic models in pdf
by Tom Goddard 20 Jun '13

20 Jun '13

Hi Matthias, I think there are many ways to get Chimera output into 3D PDF if you are willing to drop $600 on commercial software. The trouble is that you have to produce the 3d model in U3D format and then the U3D can be embedded in PDF. Those two conversion steps, going from a Chimera 3d export format such as X3D to U3D and the U3D to PDF I believe can be done by many commercial applications. But I don't know free applications to do it. There may well be free applications but it might take a whole day of digging on the web to find them. If you do find them let us know. It is easier to find a commercial software conversion route. For instance PolyTrans ($395) from Okino Computer Graphics claims to read X3D and export U3D, and Adobe Acrobat Pro X ($200) can put U3D into PDF files. http://www.okino.com/conv/filefrmt_3dexport.htm http://help.adobe.com/en_US/acrobat/X/pro/using/WS58a04a822e3e50102bd615109… I've never tried this and would definitely worry about whether PolyTrans or any other software will faithfully handle Chimera's X3D output. I think the basic problem is U3D and 3D PDF are used by almost noone. The Okino web site gives some idea of the trouble with U3D: "Okino also has a long history involved with the U3D file format. U3D has quite a tainted history in the development community. It was derived from the old Intel IFX 3D gaming toolkit of the 1990's and forced upon developers as the Macromedia 'Shockwave-3D file format' in 2000. The Shockwave-3D format was abandoned in 2002 and then it resurfaced in 2004 when Intel forced it upon Adobe as the 3D file format to use within 3D PDF files (instead of Adobe using the better X3D file format). With the IFX toolkit being so buggy, Okino spent much of 2004 through to 2007 debugging the IFX toolkit and creating the main, defacto implementation of the U3D import/export converters." The AxPyMol plug-in you mention does not produce PDF (and is commercial, $148 academic, or $404 for a lab license, 1 year subscription). It embeds 3d PyMol scenes in PowerPoint -- there is no PDF involved as far as I can tell. It uses an Active X plug-in (only available on Windows). Tom On Jun 20, 2013, at 10:29 AM, Matthias Barone wrote: > Hi Tom and Conrad > Thank you for the fast replies and sorry for not being clear: > Im doing all presentations with the beamer package of latex and hence search an interactive way to show 3D models of x-ray protein structures instead of showing pictures. > What Im therefore searching is a way to make a pdf that provides me a 3D model (incl. mouse gestures like zoom, rotate, clip) with pre-set layout (ribbon, electron density colours and so on set in chimera). > > matthias > > > > > > >>> Conrad Huang <conrad(a)cgl.ucsf.edu> 20.06.13 19.16 Uhr >>> > Collada format is used by Apple's iBooks Author program to embed 3D > graphics. Collada files, with .dae extension, can also be displayed in > Apple's Preview application. > > I don't believe Collada is at all related to PDF, which uses U3D format > for 3D data. MeshLab is supposed to read many data formats, including > Collada, and generate U3D output. Unfortunately, Chimera Collada output > is not read properly by MeshLab; triangle per-vertex colors, specified > as an RGBA data source, seem to be ignored. Worse, saving U3D output > (so at least we get the geometric shape) also fails, producing, from > Chimera's 28MB Collada file, 2 1KB files (no, I don't think it's due to > compression :-) ). > > The bottom line is that I do not have anything new to contribute on the > PDF front. Sorry. > > Conrad > > On 6/19/2013 9:43 PM, Tom Goddard wrote: > > Hi Matthias, > > > > I'm not clear on what your goal is. You talk about embedding > > molecule models in PDF, in Latex and in HTML. > > > > Conrad Huang in our lab added Collada export to Chimera so that > > molecular models could be dropped into some ebook format but I'm not > > sure if that format was PDF or something else. Have to find out from > > him. We are also working on displaying 3d views of molecules in a web > > browser using WebGL and Chimera can export an html file for that. Those > > files tend to be large and you need a web browser that supports WebGL to > > view them. The Collada and HTML export are under Chimera menu entry > > File / Export…. The Collada export is in Chimera daily builds and HTML > > export is in Chimera 1.8. > > > > Tom > > > > > > On Jun 19, 2013, at 5:41 AM, "Matthias Barone" wrote: > > > >> Hi > >> I keep on searching for a solution for embedding atomic models in pdf > >> (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, > >> but I want to use chimera. You were already discussing a similar topic > >> in > >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The > >> question in the topic was whether its possible to incorporate > >> mesh-data (via programs like MeshLab, Photoshop and the movie15 > >> package) into .tex files. > >> But Im searching for latex packages to display and manipulate atomc > >> models. Exporting in html could be a way to desplay everything but > >> electron densities (although html doesnt support mouse gestures) > >> sincerly, matthias > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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atomic models in pdf
by Matthias Barone 20 Jun '13

20 Jun '13

Hi I keep on searching for a solution for embedding atomic models in pdf (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, but I want to use chimera. You were already discussing a similar topic in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The question in the topic was whether its possible to incorporate mesh-data (via programs like MeshLab, Photoshop and the movie15 package) into .tex files. But Im searching for latex packages to display and manipulate atomc models. Exporting in html could be a way to desplay everything but electron densities (although html doesnt support mouse gestures) sincerly, matthias

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Ensemble cluster
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool. Here is the problem I face: I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters _but _the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters. May you tell me what is wrong with my understanding? Many thanks for your help, Damien ps : Is there a way to cluster according to a previously chosen RMSD?

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Command line history
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, I just installed the last release for Windows (June 07, 2013). I would like to get back the command line history I had in the previous version. I saved this command line history in a file named/chimera.cmd/. May you tell where to copy/chimera.cmd/ in the program files of my new Chimera? (I've made a search in the Windows explorer for /chimera.cmd/ but nothing was returned) Thanks, Damien

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Hydrophobicity surface
by Anne Simonsen 19 Jun '13

19 Jun '13

Dear Chimera helpers, I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice? Thank you! Best wishes, Anne -- Anne Simonsen, PhD, Professor Dept. of Biochemistry, Institute of Basic Medical Sciences University of Oslo, P.B. 1112 Blindern 0317 Oslo, Norway Visiting address: Domus Medica, room 3174 Sognsvannsveien 9 0372 Oslo Phone: +47 22 851110 Fax: +47 22 851058 Mobile: +47 99350960 email: anne.simonsen(a)medisin.uio.no http://www.med.uio.no/imb/english/research/groups/autophagy/

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adding an O in compound 1
by Ibai Gazpio 18 Jun '13

18 Jun '13

Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.

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Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

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protein schematic representaton
by francesco oteri 13 Jun '13

13 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

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Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

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display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

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Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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