- Chimera-users - RBVI Mailing Lists

internal coordinates (z-matrix) in chimera
by Chinh Su Tran To 21 Mar '13

21 Mar '13

Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. I have bunch of conformations, so I may not use the gui. Thank you. Chinh

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importing maps into chimera
by Arnaout, M. Amin,M.D. 21 Mar '13

21 Mar '13

What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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re
by Larry Simpson 21 Mar '13

21 Mar '13

Hi I have a strange problem with Chimera 1.7. My computer (Windows 7 64 bit) just had Microsoft updates last night and now Chimera does not see any drives but C and D. I usually use files on virtual drives E, etc. I tried rebooting, reinstalling Chimera but it is still the same problem. Any suggestions? Larry

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how to make super8.msf.
by han xiaodon 21 Mar '13

21 Mar '13

dear professor. would you share me how to make super8.msf.

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MSI Installer
by Yanni 20 Mar '13

20 Mar '13

Hello Do you have a chimera MSI installer available to download? Many thanks Yanni

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Re: [Chimera-users] show alpha-carbon as sphere in chimera
by Elaine Meng 19 Mar '13

19 Mar '13

On Mar 18, 2013, at 8:07 PM, Feixia wrote: > Hi Elaine, > Is there a way to show alpha-carbon only in Chimera as sphere? I can show beta-carbon, but always together with alpha-carbon. Alpha-carbon for some reason doesn't show by itself. Thanks a lot. > Best, > Feixia Hi Feixia, Maybe you are also displaying ribbon. By default when the ribbon is shown, the alpha-carbon will not show. You can allow showing both ribbon and alpha-carbon with command: ribbackbone <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> However, you can see the "real" position of the alpha-carbon is not exactly on the ribbon. Sometimes it will seem to float away, and the image might not look good. That is because the default ribbon is a smooth interpolation. Possible ways to handle this issue: (a) don't show ribbon (b) make the alpha-carbon sphere(s) big enough and/or change the viewing angle so it is not obviously floating away from the ribbon. Whether this is possible depends on which positions you are displaying and the specific backbone conformation in those areas. (c) change the ribbon from the default B-spline to cardinal spline, with or without some compromise smoothing, for example with commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> More discussion/explanation of this issue: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon…> 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

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Fwd: Re: Version 1.7 on linux
by Greg Couch 19 Mar '13

19 Mar '13

(Forgot to reply to list as well.) Hi Austin, What's your alias? chimera should *not* be on your PATH, it expects to find its version of various system libraries. Instead put a symbolic link to CHIMERA/bin/chimera in one of the directories on your PATH. Not sure what you mean about two threads, a screenshot would help. HTH, Greg On 03/19/2013 12:31 PM, Austin B. Yongye wrote: > Hello Chimera users, > I just installed version 1.7 on my centos v5.4 machine. When I launch > it using an alias, there is a splash across my entire screen and two > threads are shown on the bottom panel. This splash persists for long, > and I get the usual GUI only after switching between the two threads a > couple of times. When I proceed to open a structure, nothing shows up > on the GUI though it says a structure has been opened. > All these problems go away when I launch chimera directly from the > installation directory. > Any suggestions? Thanks. > Austin- > >

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How to change water molecule from triangle stick to folded line stick?
by 강현아 19 Mar '13

19 Mar '13

Hello, Chimera Users! I am just a beginner and haven’t learned much about Chimera. When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape. Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick) But, they are still triangle. It looks like there is H-H covalent bond in H2O. How can I remove this unwanted bond? Is there any other option for molecule shape? Like licorice… Please let me know how can I draw water with folded line stick shape, not triangle. Thanks in advance. Best regards, Hyeona Kang

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simple question
by Francesco Malatesta 19 Mar '13

19 Mar '13

Hello I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? thank you very much Francesco Malatesta

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Colors of van der Waals speheres
by Rosa Miralles 19 Mar '13

19 Mar '13

Hi, I would like to create an image with van der Waals radii colored in only one color instead of being colored as the corresponding atoms. Is it possible to choose the color of the van der Waals spheres? Thanks for your help, Rosa.

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Import Chimera Modules
by Jonathan Williams 18 Mar '13

18 Mar '13

Hello, I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html) and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: >>> import chimeraInit >>> chimeraInit.init([]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. Any help or advice would be greatly appreciated, Jon Williams

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Transparent single atoms when rendering stereoimages
by Rebecca Swett 18 Mar '13

18 Mar '13

Hi, i'm rendering some peptides structures that have single magnesium and manganese atoms in frame, and when I save the images as a stereopair, the atoms render as transparent, with protein ribbon showing through. I've tried several different colors on this, I think it's just a bug. The tips of sidechains also are transparent where the atoms are showing. I"m using the windows 64 bit build, in 1.7, downloaded today. -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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define plane question
by Steven Waldauer 16 Mar '13

16 Mar '13

Hi Everyone, Hopefully this isn't a stupid question. I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined? For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation. Thanks, Steve

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chimera and modeller
by Tomek Wlodarski 15 Mar '13

15 Mar '13

Hi! I am trying to run Modeller from Chimera (Model/Refine Loops). I have downloaded the newest version of both, and I can run Modeller as a stand alone software via python. As a location of Modeller exe I put: /usr/lib/modeller9.11/bin/mod9.11 however when I try to run this it does nothing... Status is "completed" while State is "running" and Run time is (-). On the other hand I can run via Modeller server.. When I tried to run /usr/lib/modeller9.11/bin/mod9.11 I got: FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation Any ideas or suggestions? Thanks a lot! Best! tomek

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structure
by Gonzalez, Mireya 15 Mar '13

15 Mar '13

To whom it should concern I am using your chimera on a specific protein that has/display 8 chains (A,B,C,D,E,F,G,H) with the same sequence. I would like to know how to hide the chains so I can work with one chain at a time in order to see where exactly my compound is binding so I can get the amino acid domain. Any help with this matter will be greatly appreciated. Dr. Mireya Gonzalez-Begne Research Assistant Professor University of Rochester Center for Oral Biology 601 Elmwood Ave. Rochester, NY Telephone: (585)273-1424

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3 DAYS! autoPACK Visualization Challenge: HIV in Blood Plasma due March 18
by Graham Johnson (qb3＠UCSF) 15 Mar '13

15 Mar '13

Autodesk unites with UCSF and TSRI to challenge you to explore the mysterious world of HIV in vivo. We will provide competitors with a cellPACK model of HIV in blood plasma and a powerful open source app, called autoPACK. It is up to you to convey humanity's complex relationships with this virus, be they emotional, political, or intellectual. We need your help to excite general audiences with visuals that will help us spread interest in the search for a cure. We challenge you to use the animation tools available in Chimera, namely the new Animation GUI (Tools>Utilities>Animation), to create a movie and submit it to the challenge. You may submit to any of the following categories: • Open Video: (grand prize $2,500 cash) competing against professional animators who are 3 months in • Open Image: (grand prize $1,500 cash) competing against professional artists who are 3 months in • Newly opened, 3 day long, Molecular-Viewer-Only: ($250, 3D print of HIV model, and AMD graphics card) competing strictly against other Chimera or PMV users only. Critical details on the following pages will help you get started immediately: 1) General challenge site: http://www.autopack.org/cellpackchallenge2012 2) Overview, installation, and animation instructions for Chimera-autoPACK: http://www.autopack.org/documentation/tutorials/molecular-viewers 3) Official autoPACK Visualization Challenge website to register and enter for free: http://autopack.cgsociety.org 4) Full prize details: http://autopack.cgsociety.org/autopack/prizes Please let me know if you have any questions and good luck! Graham Graham Johnson PhD qb3@UCSF Fellow UCSF Lab: http://mesoscope.org Medical Illustration: http://grahamj.com Enter the autoPACK Visualization Challenge! Ends March 18 http://autopack.cgsociety.org

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Reduce mesh density?
by Maja Divjak 13 Mar '13

13 Mar '13

Hello Chimera, I would like to export some protein models in obj format and I was wondering if there is some way of reducing the mesh complexity when I do that please? I am using the models for animations in Maya and when I use the mesh reduce feature in Maya, Im getting some rather odd results, so was wondering if I can actually simplify the models first in Chimera? Thank you for your time, Maja Divjak Walter and Eliza Hall Institute, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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Re: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it?
by Elaine Meng 11 Mar '13

11 Mar '13

Hi Boaz, Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS). Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits. After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example. Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog. That option was just provided for convenience because people often like to evaluate pocket hydrophobicity. 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 Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote: > Hi, > I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane? > Thanks for your input. > Boaz

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ViewDock: flexible receptor residues in different chains
by Jérôme Hénin 11 Mar '13

11 Mar '13

Hi everyone, When viewing Autodock Vina results in ViewDock, I hit a problem that I think is due to insufficient parsing of the PDBQT file. I have flexible receptor residues in two identical chains, say, Leu15 in chain A and Leu15 in chain B - these sidechains are part of the PDBQT file. However, ViewDock apparently ignores chain identifiers in that file, so it is unable to distinguish between these two residues, and it creates mangled bonds linking them while some other bonds are missing. I don't know how much work it would be to parse chain identifiers from the PDBQT file, I would have a go at it if I was more of a Python person, but I really am not. Best, Jerome

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Re: [Chimera-users] internal coordinates (z-matrix) in chimera (Chinh Su Tran To)
by Visvaldas K. 08 Mar '13

08 Mar '13

Dear Chinh, I am not sure if you can do multiple (batch) conversions in chimera, but the tool you seek could be openbabel, using command line or openbabel gui. On the command line you can issue, for one molecule (it's for Linux): babel my.mol my.gzmat This creates Gaussian style Bond-Angle-Torsion a.k.a. Z-matrix coordinates. For batch processing, you can use: babel *.mol -ozmat -m Best regards, Vis

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comparing angles in 28 structures
by Elaine Meng 08 Mar '13

08 Mar '13

Hi Paola, Other than measuring the angle in each one, the only other idea I have is to open the 28 structures as a single trajectory in the MD Movie tool. You can only do that if each file has the same atoms with the same names. Then you can plot the angle across the 28 "frames" in the trajectory. However, if the structures do not have the exactly the same atoms, I don't know any other method than opening and measuring each one individually. There are several trajectory input options including multiple PDB files, although in that case you would need to give the files names including numbers and ending in ".pdb". The MD Movie tool including input options is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h…> After you open the trajectory, you can use the MD Movie controller to "play" through the 28 frames. You can plot values such as the angle of interest, see the MD Movie menu: Analysis.... Plot <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#p…> 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 P.S. this is a "user" question, so chimera-users(a)cgl.ucsf.edu (CC'd here) is a better place to send it than chimera-dev, which is for programming questions On Feb 21, 2013, at 12:30 PM, Paola Peshkepija wrote: > Good afternoon, > I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. > Thank you in advance for your help! > Paola

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Chimera Tutorial in Boston area
by Scooter Morris 06 Mar '13

06 Mar '13

Hi all, I'll be teaching a Chimera tutorial scheduled as part of the VizBI conference <http://vizbi.org/2013/> in Cambridge, MA. See the Program <http://vizbi.org/2013/Program/> for information about what we'll be covering, or just bring your favorite structure and we'll explore some of Chimera's new features. -- scooter

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Re: [Chimera-users] How to fork/specify a web browser
by Greg Couch 06 Mar '13

06 Mar '13

Forgot to include list in reply. -------- Original Message -------- Subject: Re: [Chimera-users] How to fork/specify a web browser Date: Wed, 6 Mar 2013 09:23:11 -0800 From: gregc(a)cgl.ucsf.edu To: Yasha Karant <ykarant(a)csusb.edu> > For certain of the tutorials, help files, etc., Chimera linux displays a > comment to use a web browser in order to use a URL file://foobar . > How does one configure Chimera to automatically use a specified browser > to diplay the URL generated by Chimera? I have not been able to find a > preferences setting for this, nor an answer on the web or in the Chimera > manuals/help. I have not perused the source code for Chimera to find a > solution. > > Yasha Karant > Chimera uses Python 2.7's webbrowser module to open files in a web browser. For Linux, if you are using a GNOME or KDE desktop environment, then it will use the default browser that is configured for that environment. Otherwise, it looks for firefox (and derivatives), kfm, konqueror, galeon, epiphany, skipstone, opera, mosaic, and grail(!). You can override the the search order with the BROWSER environment variable. You may have noticed that Google's chrome is not on that list. Chrome support is included in Python 3's webbrowser module. But, that support would only be needed if you are not using a GNOME or KDE desktop environment. I will look into how much work it would be to backport Python 3's webbrowser module to Chimera. HTH, Greg

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How to fork/specify a web browser
by Yasha Karant 05 Mar '13

05 Mar '13

For certain of the tutorials, help files, etc., Chimera linux displays a comment to use a web browser in order to use a URL file://foobar . How does one configure Chimera to automatically use a specified browser to diplay the URL generated by Chimera? I have not been able to find a preferences setting for this, nor an answer on the web or in the Chimera manuals/help. I have not perused the source code for Chimera to find a solution. Yasha Karant

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Guessing net charge
by Miro Moman 05 Mar '13

05 Mar '13

Hello, When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Best regards, Miro Moman -- http://www.e-moman.eu

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