- Chimera-users - RBVI Mailing Lists

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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sgi core dump
by bala 27 Sep '07

27 Sep '07

Dear chimerians, Goodday. I installed the latest-chimera for sgi irix. Installation was completed successfully. But when i give chimera, it throws the following core.. Kindly write me how to get rid of the same. ce/BPT/RangeErr/DivZero/Ovflow trap (core dumped) thanks, Bala

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Docking of PDB data
by Alexander Solodukhin 19 Sep '07

19 Sep '07

Dear Listers, I have got the CCP4 3d map of PKC created from tilted series of 2d crystals grown on lipid monolayers. Unit cell: a=b=53A, alpha=beta=90 deg and gamma=120 deg. X-rays 3d structures of three fragments: C1b, C2 of the regulatory domain and catalytic domain are available from PDB data bank. When I try to dock PDB files or their maps created with SPIDER or SITUS programs by the use of 'fit models in maps' or 'fit maps in maps' in CHIMERA, programs place this fragments into one only place around the point that looks like a 'center of gravity' of CCP4 model. If I cut off the part of model where this point is, anyway program places these fragments into the same point out of the selected subregion. How can I fix this problem? I understand that I have to assign the same origin of coordinates for my model and fragments, but I do not know how to do this. Alexander Solodukhin, Ph.D. Department of Anesthesiology University of Virginia Health System P.O.Box 800710 Charlottesville VA 22906-0710

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Molecular surface crash
by Thomas Goddard 13 Sep '07

13 Sep '07

Hi Markus, I computed a molecular surface for the PDB file you gave me by changing the probe radius from 1.4 A to 1.399 A. I set the new probe radius using the "New Surface" category of the Preferences dialog (menu Favorites / Preferences). The "New Surface" category was added in Chimera 1.2430 (July 23, 2007) so you'll need the newest Chimera snapshot on Linux http://www.cgl.ucsf.edu/chimera/download.html#snapshots or a weekly Chimera build (very latest code) on other platforms (Mac, Windows) http://www.cgl.ucsf.edu/chimera/alpha-downloads.html New Chimera surface calculation code is still 6 months away. Tom Markus Voehler wrote: > Tom > > I have switched from my SGI to a RHEL 5 machine and see the same > behavior now on that computer as I have seen on the Mac. Some pdb files > do not seem to allow me to show the surface plot. This leaves me with no > option to display the surface for some pdb's. In the past I was just > doing this work on the SGI, which worked fine. I have tried your > suggestion about increasing the vdv radius again on the Linux box, but > it did not help either on this computer. Has there been any resolution > to the mentioned report 1295? > > I have deposited the pdb online, in case you want to reproduce the > problem on your cpu. The link is: > > [deleted] > > Any help is appreciated. > > Markus >

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When structures and density maps don't align
by Walter R.P. Novak 10 Sep '07

10 Sep '07

Hi All, Amongst my colleagues (to whom I constantly evangelize Chimera) there is often an issue opening pdb and map files together. Specifically, sometimes the maps and pdb coordinates are not superimposed (often drastically). I have been able to reproduce the issue so let me explain what works and what doesn't. What works: If you take a pdb file and an mtz into Phaser (from the ccp4 suite) then refmac for rigid body refinement and convert the output mtz to a map using mapman it works. The pdb and map superimpose perfectly. What doesn't work: If you take a pdb file (of known correct solution but not transformed to the correct coordinates) and throw it into refmac (ccp4) and do some rigid body refinement and then convert the resulting mtz into a ccp4 map, the map is perfectly good (the statistics are identical to using the phaser placed model), but when opened in Chimera they do not superimpose. Both of the methods above appear valid as far as structure determination (R and Rfree are identical, etc) and I know coot will align the model and map and I believe pymol will too, though I don't use pymol personally so I cannot vouch for that. Is the correct transformation information hidden in a file somewhere so that Chimera can align the two files automatically. Often people skip the phaser step and drop the model right into refinement and then manually aligning in Chimera becomes difficult. Best, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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