Dear all, I know how to change the size of the balls using the vdwdefine, but I don't see the command/option to change the diameter of the cylinder in bs representation. Can I do this? best JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dijous, Maig 7, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 7

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Today's Topics:

1. Re: chimera performance (Greg Couch) 2. volume filtering (Thomas C. Marlovits) 3. Re: volume filtering (Tom Goddard) 4. Re: any aid for dock3.5 score? (Elaine Meng) 5. Re: chimera performance (Bala subramanian) 6. Re: chimera performance (Greg Couch)

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Message: 1 Date: Wed, 6 May 2009 12:23:38 -0700 (PDT) From: Greg Couch <gregc@cgl.ucsf.edu> Subject: Re: [Chimera-users] chimera performance To: Bala subramanian <bala.biophysics@gmail.com> Cc: chimera-users@cgl.ucsf.edu Message-ID: <Pine.OSF.4.63.0905061215200.1920327@guanine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

On Wed, 6 May 2009, Bala subramanian wrote:

...

Friends,

Is there any way to check the performance of chimera. I have been using> chimera without any problems but now it is very slow, in opening even a small dna molecule and manipulating. Is there any way that i can check the root of the problem.

Thanks, Bala

So it was formerly fast on the same computer? This could happen on a Linux computer if you updated the kernel and forgot to reinstall the graphics driver (from ATI or NVidia, the open source 3D drivers still need work, but are improving). Another possibility, on all operatings sytems, is that there is a background process that is using a lot of CPU or memory, so chimera doesn't have the resources it used to.

If you just want to check the graphics performance, then you can use the Benchmark tool in Tool / Utilities to guage the current performance. And then you can compare to the reported scores to see if your graphics performance is reasonable (the Show button in the Benchmark tool brings up the web page).

- Greg

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Message: 2 Date: Tue, 5 May 2009 22:34:45 +0200 From: "Thomas C. Marlovits" <marlovits@imp.ac.at> Subject: [Chimera-users] volume filtering To: <chimera-users@cgl.ucsf.edu> Message-ID: <019F22EC-BFF8-4612-A1B9-BE4DDA9471E3@imp.ac.at> Content-Type: text/plain; charset="us-ascii"

HI,

I am trying to look for the various filtering options as descibed on the Chimera webpage (guide to volume data display). Indicated are Gaussian filtering, Fourier filter, Hide dust, etc ... unfortunately, I can only find the Gaussian filter option under TOOLS/VOLUME DATA

but cannot find the others ... can you point me to these other options, in particular the Fourier filter ? (am using version 1.3 !) Tx. -Thomas

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Thomas C. Marlovits, PhD, M.A.S. Research Group Leader

IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA)

Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe

fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits@imp.univie.ac.at