April 2015 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] Using Chimera to display family shuffling information.
by Elaine Meng 10 Apr '15

10 Apr '15

On Apr 8, 2015, at 5:11 PM, Matthew Tiffany <matt.tiffany(a)icloud.com> wrote: > To Whom It May Concern: > I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html > > What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself. > > Regards, > Matthew Tiffany > Postdoctoral Fellow > Mark A. Kay Laboratory > Stanford University Hi Matthew, I’ve CC’d the chimera-users list since my answer doesn’t involve programming... Chimera itself includes a lot of sequence-structure interactivity and related features. Certainly you could do it semi-manually: (1) open your 3D structure and sequence alignment in Chimera. You can just the “File… Open” dailog. Chimera understands several sequence alignment formats. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> (2) associate the structure with a sequence in the alignment. I don’t know exactly what your data look like, and so this requires some judgment calls and deciding amongst different strategies. My thought is at least initially, don’t worry about which sequence is associated with the structure, just try to get it associated with any sequence so that the 3D mapping along the alignment as a whole is correct. — approach A: just use sequence window menu Structure… Associations to force association with any one of the sequences, if it didn’t already associate automatically — approach B: add the sequence of the chimeric protein to your sequence alignment, sequence window menu Edit… Add Sequence, use From Structure (if it adds it poorly you may have to go through a few cycles of Edit… Delete Sequences/Gaps to remove it and then adding it back with different alignment parameters) … I’m leaning toward approach B as the better approach, but you can see whether one or the other works better for your situation… <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> (3) then you can select the different parts of the structure for coloring by using the mouse in the sequence window to select the appropriate ranges of residues in the structure-associated sequence <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Another approach to #1-2 above would be to start with a sequence of just your structure (for example, open the structure, use Favorites… Sequence to show its sequence) and Blast against the PDB, then load in the Blast alignment. However, you already have your own alignment so I don’t think it would get you much further. Further, there is a newish “mda” command that performs multiple steps including blasting against PDB, automatically loading in the structures and Blast alignment, and conveniently laying out the structure hits N->C (based on alignment to query) in the 3D display. This also wouldn’t get you much further toward the color mapping of your chimeric structure, but the layout stuff is cool. It might not work if your shuffled cassettes are pretty short though. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html> 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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Atomspec balloon don't show up
by LINA MARCELA PEDRAZA CASTILLO 09 Apr '15

09 Apr '15

Hi. (Sorry about my english, it's not my language) Dear users: I'm working on my thesis, and I use Chimera ucsf for everything, and suddenly, one day, it stops showing the atomspec balloons, (when the cursor is paused over an object (atom, bond, surface, *etc.*), whether to show the corresponding label information in a balloon in the graphics window, and PDB chain information, if available, in the status line <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html#statusli…>.) OK, That's what's no happening anymore, and I need it, so... Can you help me please with this issue? I already read the docs and I did the modifications at preferences menu, and modify: Labels *Label font* (*Sans Serif* - *Normal -* *16* *Labels on top* (*true* *Show atomspec balloon* (*true* *Atomspec display style* (*simple* Please, help me with this. Thanks. I will appreciate it.

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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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Chimera-users April 2015