- Chimera-users - RBVI Mailing Lists

deleting entries from rapid access list (plain text format)
by Boaz Shaanan 02 Apr '13

02 Apr '13

Hi, Is there a way to delete entries from the rapid access list without having to edit the preferences file? If there isn't such a way, is it possible to request to add such feature? Thanks, 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

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Weird looking stretch in ribbon presentation
by Boaz Shaanan 30 Mar '13

30 Mar '13

Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, 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

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distance label decimal places
by matheus froeyen 28 Mar '13

28 Mar '13

Hi, does someone know how I can control the number of decimal places shown in a distance label using the command line? thanks! mathy

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transparency command unrecognized
by Corey Fugate 28 Mar '13

28 Mar '13

I am following the Chimera Movie Making tutorial, but when I use the command "transp 80,r" the command line tells me, "Unrecognized command: "transp". I tried replacing "transp" with "transparency" and got the same result. Can someone explain to me why this isn't working? (I'm using build 1.5.3 on my MacBook. Thanks, Corey

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Reg: Hydrogen Bond Analysis
by Amit Jaiswal 27 Mar '13

27 Mar '13

Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. ~~~~~~~~~~~~~~~~~~~~~~~~~

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sphere representation for specific atoms
by Xiongzhuo Gao 27 Mar '13

27 Mar '13

Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen

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need help
by Hira Saleem 25 Mar '13

25 Mar '13

Respected fellows! i need help from you. actually i am working on my project and uses chimera for this . i have a problem because i have a huge data and i have to collect RMSD value of 10000 pdb ids in a 262 by 262 matrix. just wanted to know if there is another procedure to collect value instead of collecting manually. because it takes too much time and very hectic work. waiting for your precious suggestion and will be very thankful to you.

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torsion angles to x,y,z coordinate
by Chinh Su Tran To 24 Mar '13

24 Mar '13

Dear Chimera users, I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations) Is it possible to do that in Chimera? Please help. Thank you. Chinh

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3D projection of eigen vectors
by Prasanna Venkatesh 22 Mar '13

22 Mar '13

Dear support member, I would like to know the steps or command lines that I should follow to make 3D projection of eigen vectors like Tube representation or porcupine plots in Chimera. Thank you in advance. Regards, Prasanna Ph.D student Ajou university, South Korea

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internal coordinates (z-matrix) in chimera
by Chinh Su Tran To 22 Mar '13

22 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. 22 Mar '13

22 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 20 Mar '13

20 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 16 Mar '13

16 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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