- Chimera-users - RBVI Mailing Lists

benchmark scores
by Waterman, DG (David) 06 Sep '07

06 Sep '07

Hi, My info: Graphics - NVIDIA Quadro NVS 285 Processors - 2 Intel Pentium 4 Clock (MHz) - 3400 OS Type - Windows Surface - 261 Mesh - 116 Contour - 144 Solid - 110 Recolor - 95 Notes - Test Date - 04 sept 2007 Chimera Version - 2422 Machine - Dell Precision WorkStation 380 Graphics Memory (Mb) - 64 Main Memory (Mb) - 1024 OS Version - XP Professional, 5.1.2600 Service Pack 2 Build 2600 Driver Version - 7.1.8.4 Host name Dr. Dave's computer The machine isn't that bad, I guess it is let down by a poor graphics card. Cheers, D David Waterman Post-Doctoral Research Associate Macromolecular Crystallography +44(0)1235 778722 Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom <DIV><FONT size="1" color="gray">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom </FONT></DIV>

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soliciting chain-trace opinions
by Eric Pettersen 05 Sep '07

05 Sep '07

Hi all, Right now, if you do the "chain trace" action (or type "chain @ca") Chimera shows carbon alphas and any inter-residue connectivity of those residues, including disulfide linkages. I'd like to know if users generally like this behavior or would instead prefer a "strict" backbone-only trace, so I can determine whether to change the behavior, offer both alternatives, or leave things alone. This is only really relevant to the "trace" depiction since although the "full" and "minimal" backbone depictions also show disulfides, that can be turned off by turning off auto-chaining via the Model Panel, Selection Inspector, or "setattr" command*. So what do people think? --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu * in the setattr command you would be setting "autochain" to false.

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selection of some chain but not some particular residue
by Dhiraj Srivastava 05 Sep '07

05 Sep '07

Hi All I am new to Chimera and i have hard time finding commands like how to select some chain and exclude 1 or 2 residue in that chain? also i have a protein with 2 chain. how can i make different model for different chain or different portion of same chain so i can perform some action like clipping on these model independentaly? can any one please help me for these problems? Thank you -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153

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(no subject)
by Wang, Xuelin 05 Sep '07

05 Sep '07

Dear Chimera's users: I have a problem to make an Amber MD movie using Chimera. I am sure I used the right Amber top file and mdcrd file, since I can use VMD to display them. In my trajectory file, I already striped water and counter-ions. Only box information was left with trajectory. However, when I display trajectory, all trajectories were out of shape. I saw the similar thing when I used VMD to display the trajectory without including PBC option. I doubt that there is something wrong with box information. But I don't know how to fix it. Any ideas? Thanks Xuelin

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problem while readin .phi file
by Urszula Uciechowska 05 Sep '07

05 Sep '07

Dear chimera users, I am trying to open my .phi file in chimera, but i am getting this message on the reply log: pbsa.phi: Record size at end of record 538976288 != size at head of record 20 it is becouse my file is too big? Thanks in advance! Ula -- MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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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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