August 2007 - Chimera-users - RBVI Mailing Lists

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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Vista compatibility
by Forbes J. Burkowski 30 Aug '07

30 Aug '07

Hi: Does anyone have any information about Chimera running on the Vista OS (specifically the 64-bit version)? Thanks in advance. Forbes Burkowski

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chimera on AMD workstation-> followup
by Vinay Kumar 30 Aug '07

30 Aug '07

Hello Tom and other list members, Your suggestion proved right. Chimera is installed and working well. Thankyou. Vinay On 8/10/07, Thomas Goddard <goddard(a)cgl.ucsf.edu> wrote: > > Hi Vinay, > > The chimera-1.2422-linux_x86_64.exe distribution is for 64-bit > versions of Linux. If you are using a 32-bit linux (even with a 64-bit > processor) then you need chimera-1.2422-linux.exe instead. > > If that is not the problem, could you be more specific about what > goes wrong when you try to install? What is the error message? > > Tom >

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(no subject)
by guiqing＠mailer.sb.fsu.edu 27 Aug '07

27 Aug '07

If I manually move and rotate the object in Chimera, how could I know the exact displacements along x, y, z and the rotation angle? Anyone has any suggestion? Thank you! Guiqing ----------------------------------------------------------------

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input file to make movie
by shivesh kumar 27 Aug '07

27 Aug '07

Dear all I am using chimera very first time.I want to know how to make the input files from .pdb file to make a movie.Thanx in advance for the suggestions. Shivesh Kumar

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Installing Chimera
by John Beale 27 Aug '07

27 Aug '07

I have a LINUX computer on which I have been running Chimera for a couple of years. On this system installing Chimera was very straightforward- just click on the executable. I just took delivery on a new Linux system and I have been trying to install Chimera. I downloaded the file from your site (an *.exe file). When I click on the executable my system tells me that the file had been downloaded as an MS/DOS file and I should open the file some other way. The executable would not run. I have no idea what to do with this. Can you suggest a solution? It is strange because it was so easy to install on my previous system. (I am using RedHat Enterprise LINUX). Thank You! John Beale jbeale(a)stlcop.edu

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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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Chimera-users August 2007