- Chimera-users - RBVI Mailing Lists

benchmark results 1.2422-linux_x86_64
by Damir Perisa 23 Aug '07

23 Aug '07

hi there, i just set up my new laptop with archlinux 64bit and since i'm going to use everything 64bit on this machine (no 32bit libraries), i tried first time chimera 64bit. details on machine: Thinkpad x61t (Tablet Laptop) Linux Apollon 2.6.22-ARCH #1 SMP PREEMPT Wed Aug 15 22:51:57 CEST 2007 x86_64 Intel(R) Core(TM)2 Duo CPU L7500 @ 1.60GHz GenuineIntel GNU/Linux graphics: Intel integrated graphics 965GM VideoRam: 262144 KB (xorg version 1.3.0 xf86-video-intel version 2.1.1) ram total: [damir@Apollon ~]$ free total used free shared buffers cached Mem: 1002364 570780 431584 0 9524 142080 -/+ buffers/cache: 419176 583188 Swap: 979924 372324 607600 benchmarks: surface 130 mesh 129 contour 158 solid 128 recolor 129 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 762.0 677.0 150.0 150.0 736.0 109.0 7634.0 1YTI (798): 981.0 554.0 50.0 48.0 702.0 36.0 2305.0 2GBP (2575): 877.0 375.0 17.0 17.0 609.0 16.0 713.0 1GOT (6449): 601.0 213.0 6.0 6.0 468.0 9.0 216.0 2HMG (12189): 254.0 134.0 3.0 3.0 291.0 6.0 87.0 2PDA (18894): 165.0 91.0 2.0 2.0 191.0 4.0 51.0 1YNJ (24369): 132.0 67.0 5.0 10.0 217.0 3.0 40.0 1F4H (33805): 97.0 53.0 1.0 1.0 128.0 2.0 28.0 quite low scores, no? ... in addition i'm observing that only 50% of cpu is used (means only one core). chimera is not multi-threaded? greetings, Damir

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A problem
by EFFICIENT ECON AND ENVIR FRIENDLY PRD OF KEY INTER OFMJ ANTI 22 Aug '07

22 Aug '07

Dear Sir/Madam, I am very interested in your UCSF Chimera. Unfortunately I don't know how to use it to open my PDB files derived from molecular modelling. Could you help me? Your reply will be greatly appreciated. Best wishes, Qi Zhang ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk

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copy and paste a model
by William Jeffrey Triffo 22 Aug '07

22 Aug '07

is there a way to 'copy and paste' an entire model? for example, I have a volume data map with some surface and volume renderings that I would like to display in a few different orientations (same map, maybe rotated by 45 deg) side by side in the same scene/window. -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Fitting informations
by Magali Cottevieille 21 Aug '07

21 Aug '07

Hi, Could you tell me where I can find informations of the fitting procedure of Chimera (Fit model in map)? I would particularly like to know if it is in real or Fourier space. Thank you, Magali.

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stereo view
by Rutledge, Robert (NIH/NCI) [V] 21 Aug '07

21 Aug '07

I have been trying to get chimera to work with stereo. I now have an NVidia Quadro FX 1500 card, and I start Chimera with the --stereo option. The program starts fine, but produces the following error: "can not open camera mode". Stereo will not work when I try to select it from the camera tab. My computer has 3 monitors; two are connected to the Quadro card. The first monitor (the one active during boot) is connected to an NVidia 7800GTX. Do I need to swap my cards so that the Quadro becomes the first card or is there another solution? Thanks, Robert Rutledge

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New benchmark
by David Konerding 21 Aug '07

21 Aug '07

Hello, here is a new benchmark HP xw9400 2 dual core Opteron 2220 8GB RAM Quadro FX3500 256MB nvidia driver 100.14.11 Chimera version 2422 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 15318.0 12309.0 1401.0 1313.0 15107.0 3208.0 6848.0 1YTI (798): 8422.0 7090.0 469.0 453.0 11649.0 900.0 2585.0 2GBP (2575): 448.0 2287.0 122.0 127.0 1443.0 289.0 536.0 1GOT (6449): 172.0 559.0 39.0 43.0 590.0 87.0 186.0 2HMG (12189): 173.0 254.0 26.0 27.0 246.0 52.0 78.0 2PDA (18894): 96.0 172.0 18.0 14.0 208.0 33.0 40.0 1YNJ (24369): 75.0 128.0 14.0 13.0 184.0 24.0 30.0 1F4H (33805): 46.0 114.0 9.0 8.0 72.0 25.0 21.0 surface 842 mesh 846 contour 153 solid 477 recolor 153 Dave

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VRML output
by Andrew Carter 17 Aug '07

17 Aug '07

I have been testing the vrml output from chimera (for loading into cinema 4d) and I can get a ribbon representation to work ok. However when I try a surface rendering it looses all the color. Am I dong something wrong. Also with the surface rendering is there a way to change how course the vrml output is? Many thanks Andrew

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potential bug in saving sessions using IMOD import
by William Jeffrey Triffo 17 Aug '07

17 Aug '07

not sure if this has already been reported, but if I save a session in which I have imported IMOD models (surface meshes + contours), and then reload the session, only the contours appear - the surface meshes do not. this is using build 2416, May 30 2007 release. -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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NRAMM workshop
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Scooter, Bridget Carragher suggests I give a demo of Chimera at the NRAMM (National resource for automated molecular microscopy) workshop on November 14. I think I will do that. Do you have special interest in talking with Bridget and Clint Potter about our proposed collaboration to use Chimera as a viewer of their EM database? Tom Bridget Carragher wrote: > Hi Tom, > We are hoping that we might be able to persuade you to come to our > upcoming workshop: "Workshop on advanced topics in EM structure > determination" which will be held during November 10-16, 2007 at NRAMM. > We will have a number of afternoon demonstrations of various relevant > software and we would be delighted if you would agree to give a half > hour presentation of the most relevant aspects of Chimera to the cryoE > community during the afternoon of Wednesday November 14. We will of > course, cover your airfare, as well as accommodation and all meals while > you are here and we'd encourage you to stay for as much of the workshop > as you can manage. I'm attaching a draft agenda of the workshop so you > can get an idea of the basic outlay - all except the highlighted talks > are conformed. > Best regards, > Bridget and Clint > > > ------------------------------------------------------------------------ > > > ---------------------------------------------------------------------------------------------------------------------------------- > Bridget Carragher, Associate Professor > Automated Molecular Imaging Group, Department of Cell Biology > The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, > La Jolla, CA 92037 > tel: (858) 784-9070; fax: (858) 784-9090; bcarr(a)scripps.edu; > http://ami.scripps.edu > National Resource for Automated Molecular Microscopy: > http://nramm.scripps.edu > ---------------------------------------------------------------------------------------------------------------------------------- > > > >

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Re: [Chimera-users] sym command in Chimera
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Nevin, The sym command places molecule copies relative to the coordinate frame of a density map. If you do not have a density map open it will not work. The solution is to open a density map, any map will do even if it is not related to your system -- it is just providing a coordinate frame. Here's a density map (potassium ion channel electron microscope data) if you don't have one. ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1094/map/emd_1094.map.gz You'll need to uncompress it (for example, with gunzip, or on the Mac it will offer to uncompress automatically when you download it) before opening it in Chimera. Once it is open in Chimera and you use the sym command you can undisplay it with Favorites / Model Panel. You also use Model Panel to freeze the map (uncheck the "active" button) in order to make motions of the molecule generate new positions for the molecule copies. Here is why a map is needed to define a coordinate frame. You might think the positioning matrices could just be applied in the global coordinate frame. But when you rotate the Chimera models with the mouse to get a different view point, that moves all the models around in the global frame, and that would cause all the monomers to assume a new arrangement if the matrices were applied to the rotated reference model. So in order to be able to see you models from different view points without changing their relative positions the symmetries are applied relative to the coordinate frame of a density map. (Could be relative to any other model but the command was created for people fitting molecules into density maps.) If you rotate the density map and molecules together then the matrices still keep the same relative positions of the molecules. Tom Z. Nevin Gerek wrote: > > Hello, > I am having another problem with sym command. When I test on some > proteins including the example (1i84) provided in the website, I get > 'No opened volume or reference model specified" error. > I used sym and then sym #0 but they give same error. Do I need to copy > another feature for this command? Is there anyway I can fox this problem? > > Thanks again, > > > 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 <mailto:nevin.gerek@asu.edu>

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