[Chimera-users] Chimera-users Digest, Vol 108, Issue 25

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Tue Apr 24 23:52:29 PDT 2012


Elaine is correct in that newly deposited structures (since a year or so?) have to have their TLS information converted to aniso B and have those values in the appropriate place on the ATOM card. However, this was not the case for the older entries. The 1ss8 entry seems to have been refined by refmac5 from the ccp4 package. In this package there is a program called tlsanl which will do the job of converting the TLS infotmation to B-aniso. (a several seconds job) So maybe Steve could use it and thus solve his problem?



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] on behalf of chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
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To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 108, Issue 25

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Today's Topics:

   1. Re: remote session (Greg Couch)
   2. Rendering TLS information in Chimera ? (Steven Ludtke)
   3. Incomplete chain contain many dotted lines while  displaying
      (Junfeng Huang)


Message: 1
Date: Mon, 23 Apr 2012 12:05:41 -0700
From: Greg Couch <gregc at cgl.ucsf.edu>
To: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] remote session
Message-ID: <4F95A805.1080609 at cgl.ucsf.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

The error is that the OpenGL library is looking for a NVidia-specific
extention to the remote protocol and failing when it is not there.  That
is a driver bug -- it shouldn't matter what graphics driver you have on
either of the systems.  There are two things I'd do to try and fix it:
(1) try updating the NVidia driver on the remote computer that is
running chimera (not the computer displaying chimera), and (2) try
uninstalling the NVidia driver on the remote computer, and reverting to
the software implementation of OpenGL (mesa).  The first option is
preferable if it works, because the proprietary (NVidia/AMD) drivers
have been faster and less buggy than the mesa driver for most uses.

     Good luck,


On 04/20/2012 02:25 PM, Hernando J Sosa wrote:
> Hi
> I used to be able to run chimera remotely from a machine with an X-
> windows server  (the one that comes with Cygwin in this case). But now
> I get the following error:
> Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
> X Error of failed request:  BadRequest (invalid request code or no
> such operation)
>   Major opcode of failed request:  148 (GLX)
>   Minor opcode of failed request:  181 ()
>   Serial number of failed request:  12779
>   Current serial number in output stream:  12784
> I t does work fine if run directly from the computer  where chimera is
> installed. Any idea what the problem could be?
> Thanks
> Server computer:
> Chimera v 1.5 (similar problem with 1.6)
> OS: Linux OpenSuse 11.3 64b
> Client computer:
> OS: Windows 7 64.
> Graphics: ATI Radeon HD 5450
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Message: 2
Date: Tue, 24 Apr 2012 08:02:06 -0500
From: Steven Ludtke <sludtke at bcm.edu>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Rendering TLS information in Chimera ?
Message-ID: <A4949A7D-5D36-4123-842E-823247E5147F at bcm.edu>
Content-Type: text/plain; charset=us-ascii

Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ?  Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor.  However, I can't see any obvious way of rendering the TLS information.  Any tips ?

Steven Ludtke, Ph.D.
Associate Professor
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr)
Dept of Biochemistry and Mol. Biol.                    (www.bcm.edu/biochem)
Baylor College of Medicine
sludtke at bcm.edu
stevel at alumni.caltech.edu


Message: 3
Date: Tue, 24 Apr 2012 10:58:27 +0800
From: Junfeng Huang <jfhuang.dg at gmail.com>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Incomplete chain contain many dotted lines
        while   displaying
        <CAKO12g6r1EK2y+uBNyx_WbGp8mGZxFRmgwqjCrJ5Tq-W5zJQCg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Everyone?

I have a problem while display PDB file.

I extract the residues from protein-protein interface by ligplus into a new
PDB file, and want to display and analysis it. As the file contain only the
residues form interface, they are discontinuous.

While display with pymol, it is OK. However, While using Chimera, there are
many dotted lines between the residues. I know what the dotted lines are,
but I do want to hide all these lines, can somebody please give me some

I sent two figures in the attachment. It's the first time I used mail-list,
if it doesn't support figures, please check here:

Interface display by pymol

Interface display by Chimera

Thank you very much!
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