[Chimera-users] changing diameter of the cylinders in bs representation
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Fri May 8 01:34:51 PDT 2009
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 at uab.es
----- Missatge original -----
De: chimera-users-request at 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)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Wed, 6 May 2009 12:23:38 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] chimera performance
> To: Bala subramanian <bala.biophysics at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <Pine.OSF.4.63.0905061215200.1920327 at 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
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 5 May 2009 22:34:45 +0200
> From: "Thomas C. Marlovits" <marlovits at imp.ac.at>
> Subject: [Chimera-users] volume filtering
> To: <chimera-users at cgl.ucsf.edu>
> Message-ID: <019F22EC-BFF8-4612-A1B9-BE4DDA9471E3 at 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
>
>
>
> --------------------------------------------------------------------
> -----------
>
> 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 at imp.univie.ac.at
>
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Wed, 06 May 2009 13:24:13 -0700
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] volume filtering
> To: "Thomas C. Marlovits" <marlovits at imp.ac.at>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <4A01F1ED.3030808 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Thomas,
>
> You are looking at the Chimera 1.4 documentation on our web site.
>
> Chimera 1.3 is the production release (and also has documentation
> on our
> web site). To use Chimera 1.4 you need to get a daily build:
>
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>
> Tom
>
>
> Thomas C. Marlovits wrote:
> > 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
> >
> >
> >
> > ------------------------------------------------------------------
> -------------
> >
> > 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 at imp.univie.ac.at <marlovits at imp.univie.ac.at>
> >
> >
> >
> >
> > ------------------------------------------------------------------
> ------
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 6 May 2009 17:20:26 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] any aid for dock3.5 score?
> To: Francesco Pietra <chiendarret at gmail.com>
> Cc: chimera <chimera-users at cgl.ucsf.edu>
> Message-ID: <B816D602-3DB4-4888-B553-53A9BEC3F2D7 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hi Francesco,
> If by "the grid" you mean the potential map from DelPhi:
>
> If you have the academic version of DelPhi from the Honig Lab, you
> can run it with the Chimera tool DelPhiController (under Tools...
> Surface/Binding Analysis):
> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/
> delphicontroller/delphicontroller.html>
>
> This allows entering all the DelPhi run parameters and input/output
>
> filenames into a GUI instead of the text files needed to run DelPhi
>
> "manually." However, it does not help you make sure parameters are
>
> correctly assigned; you are still responsible for figuring out
> which
> DelPhi charge and radius files (also from the Honig lab) to use and
>
> making sure the atoms in your structure are named correctly to
> match
> with the parameters in these files.
>
> Also, DelPhiController is one of our older tools and may not be
> very
> easy to use.
> Elaine
> -----
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
> On May 6, 2009, at 10:14 AM, Francesco Pietra wrote:
>
> > Hi:
> > I am considering to use dock3.5 score in DOCK6.2, which makes use of
> > Delphi. Is any aid in chimera for builing the grid?
> > thanks
> > francesco
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 7 May 2009 12:08:34 +0200
> From: Bala subramanian <bala.biophysics at gmail.com>
> Subject: Re: [Chimera-users] chimera performance
> To: Greg Couch <gregc at cgl.ucsf.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID:
> <288df32a0905070308l46c44c71gded385a930a83df2 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Greg,
> You are right. Previously it was normal but now it is slow. I
> havent updated
> the kernel. I checked and noticed that i dnt have any memory intensive
> background jobs also.
>
> I did benchmarks with two chimera versions 1.3 (attached file
> chim_test) and
> chimera 1.4 (attached chim_test1).
> My graphics card is nVIDIA GETFORCE 9300MG, VRAM: 256 MB. I dnt
> know how to
> compare and judge what is going wrong. I wud appreciate your help
> on the
> same.
>
> 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: 6
> Date: Thu, 7 May 2009 11:44:34 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] chimera performance
> To: Bala subramanian <bala.biophysics at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <Pine.OSF.4.63.0905071129160.2010601 at guanine.cgl.ucsf.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Looking at your chimera benchmark scores and at the scores on the
> web
> page, http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks,
> it looks
> like you don't have the NVidia graphics driver installed. And that
> would
> make a *huge* difference. To double-check, run the glxinfo command
> and
> look at the "OpenGL renderer string:" line, it should have NVIDIA
> in it
> instead of Mesa. To get the NVidia drivers, go to
> <http://www.nvidia.com/Download/index.aspx>.
>
> - Greg
>
> On Thu, 7 May 2009, Bala subramanian wrote:
>
> > Dear Greg,
> > You are right. Previously it was normal but now it is slow. I
> havent updated
> > the kernel. I checked and noticed that i dnt have any memory
> intensive> background jobs also.
> >
> > I did benchmarks with two chimera versions 1.3 (attached file
> chim_test) and
> > chimera 1.4 (attached chim_test1).
> > My graphics card is nVIDIA GETFORCE 9300MG, VRAM: 256 MB. I dnt
> know how to
> > compare and judge what is going wrong. I wud appreciate your help
> on the
> > same.
> >
> > 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
> >>
> >
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> End of Chimera-users Digest, Vol 73, Issue 7
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