- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] How to "Align" two atoms
by Thomas Goddard 04 Oct '07

04 Oct '07

Hi Matt, Many Chimera commands are defined in chimera/share/Midas/__init__.py They are sometimes a pain to call from Python. Here is some code for the align command. Tom from chimera import openModels, selection m = openModels.list()[0] sel = selection.ItemizedSelection() sel.add(m.atoms[0:2]) from Midas import align align(sel) Matthew Baker wrote: > I'm writing a module. I've created a model and added it to the open > models. How can I reproduce the command-line function > > align #1:1 #1:2 > > The variable names for my two atoms are newModel.atoms[0] and > newModel.atoms[1]. > > Thanks, > Matt >

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Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was just searching the archieves and I understand now that my last question was alittle dumb (i.e. the x,y,z rotation angles are not helpful). In this case does the "Rotation angle" and the " Axis" define a single rotation that transforms the "Fit map" to the "with in" map. Can I draw the axis using a .bild file (i.e .arrow with start and end coords given by axis and axis point). if I want to compare several maps to one reference, is it possible to define a single axis for them all? such that i can compare them all just by the magnitude of the rotation? does this make sense? thanks in advance sean

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Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was wondering if it is possible to use the output (translation matrix, axis, ect.) from the "Fit map in map" command to obtain the angles of rotation around the x, y and z axis given an arbitrary origin (i.e. the center of the map). thanks sean

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Protein RMSD
by Beale, John 03 Oct '07

03 Oct '07

Is there any feature in Chimera that will allow the calculation of the RMSD between a protein and a reference structure? Thanks! John Beale

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updating hydrogen bonds in an MD movie
by E. Merkley 03 Oct '07

03 Oct '07

Hi Chimera crew, I am using chimera to visualize an MD trajectory. I want to look at the fluctuations of hydrogen bonding patterns in a helix over the course of the trajectory. Is there a way to use Find HBonds on each frame and display the updated pseudobonds as I view the movie in Chimera? Also, may I take this occasion to point out that requiring consecutive frames to have consecutive numbers in the file names is inconvenient. For instance, my simulation is 41 ns long, and the structures are stored (in our in-house format) every 1 ps. So rather then write out 41000 .pdb files, I'll write them out every 10 or 100 ps. To use chimera to view a movie, I have to rename the files using a perl script. Incidentally, I've been using Chimera for 3 years now and love it. -Eric Merkley Graduate student Biochemistry Department University of Washington

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chimera instalation
by Paola Beassoni 03 Oct '07

03 Oct '07

Dear all, i have downloaded chimera 1.2422 for linux and i don know hoe to install it. I have OpenSUSE but i am really new in linux. I have the file "chimera-1.2422-linux.exe" but i don know how to run it. My shell doen recognizes the command "run". So, please if anyone can help me i would really appreciate it. Best Regards Paola -- Paola Beassoni - PhD Dpto. Biologia Molecular - FCEFQyN Universidad Nacional de Rio Cuarto Río Cuarto - Argentina 00-54-358-4676422 00-54-358-4676232 (Fax)

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chimera for Amber9
by Francesco Pietra 02 Oct '07

02 Oct '07

Having installed DOCK6.1/DMS (debian Linux parallel amd64) and Chimera 1.2422 (scp-linked desktop Debian Linux i386), may I ask: 1) Can I use Chimera for Amber9 in place of VMD, which I currently use? 2) Being superficially familiar with VMD, I was looking in Chimera for *.prmtop and *.inpcrd file types, as well as rst file, etc.. I suppose I was unable to turn Chimera to use with Amber9. That said, I was very much impressed by Chimera at the first touch. Thanks francesco pietra ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Setting camera viewpoint
by Thomas Goddard 01 Oct '07

01 Oct '07

Hi Matt, There is no Chimera command to set the camera. But there are commands to orient and position the displayed models precisely (turn, move, scale, cofr, clip, savepos, reset). The Chimera world keeps the camera fixed and moves the models. If you want to use Euler angles there is a plugin to do that called Transform Molecule Coordinates available at: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom Matthew Baker wrote: > Tom, > > Is there a way of specifying a camera position and a viewing angle from > the command line in chimera. I want to make a few snapshots of a > molecule (actually, several different PDBs) with very specific view angles. > > Thanks > > Matt

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Frozen chimera
by hsosa＠aecom.yu.edu 28 Sep '07

28 Sep '07

I have the following problem: When rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash, the blue screen appear and a whole reboot is needed. The problem most likely is graphic card related. I did reported it before and was suggested to change the driver. I did but it did not solve the problem. My system currently is as follow: Chimera 1.2422 Windows XP service pack-2 Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.0027.05 ForceWare version: 78.01 Before I had: ForceWare version 91.36 So both of these video driver had problems. I wonder if anybody has experienced something similar and found the right driver. Thanks Hernando

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reconstructing x-ray structure
by Nevin Gerek 27 Sep '07

27 Sep '07

Hello, I am wondering if there is an option in Chimera to reconstruct exact place for binding peptide. I do have x-ray structures and binding peptide was incorporated as a C-terminal extension. When I used these structures, I do not get protein-peptide contact information in our model. Is there any way to reconstruct x-ray structure data with the right peptide binding information? Any help would be appreciated. Thanks. Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek(a)asu.edu

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