- Chimera-users - RBVI Mailing Lists

Mapping predicted secondary structure and solvent accessibility on structure or homology model?
by Oliver Clarke 09 Apr '15

09 Apr '15

Hi, I noticed that in the multalign sequence viewer, Chimera has the option to show predicted secondary structure, but it doesn’t seem to work, at least for my sequence (it seems to work initially, but when I show predicted helices/strands there is nothing to see). I think that incorporating modern secondary structure, solvent accessibility and disorder prediction (e.g. using JPRED, which I believe has an open API) would be a very valuable addition to Chimera for structural analysis - it would be particularly helpful for evaluating homology models and models that are based on low resolution crystallographic or CryoEM data, to pick up places where there might be a register error. Maybe this is something to consider for Chimera 2 (or maybe there is a way to load such data in now, if I could create it externally and load it in as a set of attributes…). Best, Oliver.

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openGL error.
by Mosavverul Hassan 08 Apr '15

08 Apr '15

Hi, I am trying to get chimera run remotely on a linux server while logging into it from a mac terminal. I get the following error libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1386 Current serial number in output stream: 1386 glxinfo gives me the following name of display: localhost:13.0 libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so libGL: driver does not expose __driDriverGetExtensions_swrast(): /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so: undefined symbol: __driDriverGetExtensions_swrast libGL: Can't open configuration file /mnt/raidc2/mhassan/.drirc: No such file or directory. libGL: Can't open configuration file /mnt/raidc2/mhassan/.drirc: No such file or directory. libGL error: failed to load driver: swrast display: localhost:13 screen: 0 direct rendering: No (If you want to find out why, try setting LIBGL_DEBUG=verbose) server glx vendor string: SGI server glx version string: 1.4 It seems to run fine from a linux computer but has problems with a mac. I am using X11 forwarding when I log in. I have X11 on my mac. Could someone please help me out? Regards, Mosavverul Hassan.

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problems to start chimera
by torquato.bioq＠epm.br 08 Apr '15

08 Apr '15

Dear collegues !! I'm installed chimera-1.10.1-linux_x86_64.bin on my machine witch controlled by openSUSE 13.2. The installation procedure was fine, but when I try start chimera I got this messege: ricardo@ricardolinux:~$ chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1457 Current serial number in output stream: 1457 Please can some one help T All the best Ricardo

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plane normal axis
by Elaine Meng 07 Apr '15

07 Apr '15

Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps... In my little test, the plane output information included: Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199 Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as: x 15.223 y 25.303 z 12.390 Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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 Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc. > > Thanks for all your help as always! > > Oliver.

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where is "Save each fit when doing multiple alignments" button
by sunyeping 07 Apr '15

07 Apr '15

Dear all,I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting) In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it?Best regard,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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how to measure density diameter by chimera
by Smith Liu 07 Apr '15

07 Apr '15

Dear All, Will you please tell me the command or process to measure the diameter of the molecule density in the map by chimera? Smith

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DTI stereo3D
by Dougherty, Matthew T 06 Apr '15

06 Apr '15

?When selecting DTI stereo3D, L&R images are placed side by side, and horizontally rescaled by half, known as SBS-half. I would like to generate SBS-full, ie no horizontal scaling. Is there a way to do that in chimera? Would prefer not to generate stereo pairs and rescale them back to 100% using a video editor. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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segname
by Francesco Pietra 04 Apr '15

04 Apr '15

Hello: May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes) Thanks francesco pietra

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Autodock vine problem
by Tunc Morova 04 Apr '15

04 Apr '15

Hello, I was trying to use built-in auto dock vina tool of chimera. I came a cross with an error saying service local`c:\”program filex(x86)”\”the scripps research Institute\Vina\Vina.exe` is unavailable. I have been checking forums for a longtime. Unfortunately, i couldn’t run the docking. couple days ago, I think i accidentally ran the docking locally but i am not sure. Is my pathing correct? how can my local auto dock vina be unavaible ? Please help me for finishing my thesis :D Thank you for your support -Tunc

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Opening Gromacs .trr: error with "bham_lr"
by Alan Manning 03 Apr '15

03 Apr '15

Hi I want to import a Gromacs trajectory (a .trr file) in order to create an animation. I'm using the "MD Movie" tool, and I specify the input .tpr and .trr files. However, I get the following error when I try and make the movie: Don't know correct parameters for 'bham_lr' function Does anyone know what this is from? I'm using Gromacs 5.0.4. The complete Reply Log is as follows: using memory mapping VERSION 5.0.4 using floats version 100, generation 26 2613 atoms box o water Don't know correct parameters for 'bham_lr' function Thanks! Regards, Alan Manning

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