[Chimera-users] a small suggestion

Wed May 13 03:20:35 PDT 2009

Hello everyone,

just a small suggestion to the team. Could it be possible that, when clicking on a given angle/torsion in the Structure measurments panel, the involved atom/bond get selected in the visualizer?

cheers

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: Dimarts, Maig 12, 2009 9:00 pm
Assumpte: Chimera-users Digest, Vol 73, Issue 13

> Send Chimera-users mailing list submissions to
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> 
> Today's Topics:
> 
>   1. Re: chimera performance (Greg Couch)
>   2. adding pseudo bonds (Jean Didier Pie Marechal)
>   3. Re: adding pseudo bonds (Elaine Meng)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Mon, 11 May 2009 14:32:22 -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.4.63.0905111420070.1959390 at guanine.cgl.ucsf.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> 
> I have had bad luck with NVidia drivers packaged as RPMs.  Instead 
> I 
> recommend that you uninstall the RPM you got from rpmfusion.org and 
> install the NVidia driver from NVidia at 
> <http://www.nvidia.com/Download/index.aspx>.  The "Nvidia.com 
> Binary 
> Installer" option given the webpage you cited.  As mentioned there, 
> the 
> disadvanatge of NVIdia's driver is that you need to reinstall it 
> every 
> time your update your kernel -- otherwise the X server won't start. 
> After 
> a successful install (and reboot), glxinfo should tell you which 
> OpenGL 
> renderer you have and chimera should work too.
> 
> 	Good luck,
> 
> 	Greg
> 
> On Fri, 8 May 2009, Bala subramanian wrote:
> 
> > Dear Greg,
> > After installing nvidia graphics drivers, i am not able to open 
> chimera. I
> > have attached the xconfig file and the output of glxinfo as text 
> files.>
> > *[cbala at ramana ~]$ chimera
> > Traceback (most recent call last):
> >  File "/usr/local/chimera/share/__main__.py", line 65, in <module>
> >    value = chimeraInit.init(sys.argv)
> >  File "/usr/local/chimera/share/chimeraInit.py", line 361, in init
> >    tkgui.initializeGUI(exitonquit, debug_opengl)
> >  File "CHIMERA/share/chimera/tkgui.py", line 2525, in initializeGUI
> >  File "/usr/local/chimera/lib/python2.5/site-
> packages/PIL/__init__.py",> line 309, in checkConfig
> >
> >  File "/usr/local/chimera/lib/python2.5/site-packages/Togl.py", 
> line 27, in
> > __init__
> >    Tkinter.Widget.__init__(self, master, "togl", cnf, kw)
> >  File "/usr/local/chimera/lib/python2.5/lib-tk/Tkinter.py", line 
> 1930, in
> > __init__
> >    (widgetName, self._w) + extra + self._options(cnf))
> > _tkinter.TclError: could not create rendering context
> > Couldn't configure togl widget*
> >
> > I installed the nvidia driver as follows. I installed it based on 
> the> information given in the nvidia install guide in the following 
> link.>
> > http://www.mjmwired.net/resources/mjm-fedora-nvidia.html#pci_id
> >
> > su -c 'rpm -ivh
> > http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-
> stable.noarch.rpm> '
> > su -c 'rpm -ivh
> > http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-
> release-stable.noarch.rpm
> > '
> > su -c 'rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-rpmfusion-*'
> > su -c 'yum install kmod-nvidia'
> >
> > Then i gave the following command
> >
> > nvidia-xconfig  as root. Then i restarted the system. Now i am 
> able to see
> > nvidia display setting. When i give chimera, it dosent work.
> >
> > Bala
> >
> > On Thu, May 7, 2009 at 8:44 PM, Greg Couch <gregc at cgl.ucsf.edu> 
> wrote:>
> >> 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
> >>>>
> >>>>
> >>>
> >
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 12 May 2009 17:19:46 +0200
> From: Jean Didier Pie Marechal <JeanDidier.Marechal at uab.cat>
> Subject: [Chimera-users] adding pseudo bonds
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <165553c1104b.4a09afb2 at uab.es>
> Content-Type: text/plain; charset=iso-8859-1
> 
> Dear all,
> 
> what is the way to add pseubond between metal and chelating atoms?
> if you could tell me what are the "mouse driven" and "script 
> driven" manner I'll be very pleased....
> all the best,
> JD
> 
> 
> Dr. Jean-Didier Mar?chal
> Lecturer
> Computational Biotechnological Chemistry @ Transmet
> Unitat de Qu?mica F?sica
> Departament de Qu?mica
> Universitat Aut?noma 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: Diumenge, Maig 10, 2009 9:00 pm
> Assumpte: Chimera-users Digest, Vol 73, Issue 11
> 
> > Send Chimera-users mailing list submissions to
> > 	chimera-users at cgl.ucsf.edu
> > 
> > To subscribe or unsubscribe via the World Wide Web, visit
> > 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > or, via email, send a message with subject or body 'help' to
> > 	chimera-users-request at cgl.ucsf.edu
> > 
> > You can reach the person managing the list at
> > 	chimera-users-owner at cgl.ucsf.edu
> > 
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Chimera-users digest..."
> > 
> > 
> > Today's Topics:
> > 
> >   1. Protonate heteroatoms only (Francesco Pietra)
> >   2. Re: Protonate heteroatoms only (Eric Pettersen)
> > 
> > 
> > ------------------------------------------------------------------
> --
> > --
> > 
> > Message: 1
> > Date: Sat, 9 May 2009 23:35:37 +0200
> > From: Francesco Pietra <chiendarret at gmail.com>
> > Subject: [Chimera-users] Protonate heteroatoms only
> > To: chimera <chimera-users at cgl.ucsf.edu>
> > Message-ID:
> > 	<b87c422a0905091435q4a1671e2td61284cf092e7fb6 at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> > 
> > Hi:
> > Is there a command in Chimera to protonate (Sybyl-type) the
> > heteroatoms only (or deprotonate the other elements from a fully
> > protonated protein)?
> > thanks
> > francesco pietra
> > 
> > 
> > ------------------------------
> > 
> > Message: 2
> > Date: Sat, 9 May 2009 15:27:55 -0700
> > From: Eric Pettersen <pett at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Protonate heteroatoms only
> > To: Francesco Pietra <chiendarret at gmail.com>
> > Cc: chimera <chimera-users at cgl.ucsf.edu>
> > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30 at cgl.ucsf.edu>
> > Content-Type: text/plain; charset=US-ASCII; format=flowed
> > 
> > del HC
> > 
> > will delete all hydrogens bonded to carbons (their IDATM types 
> are 
> > HC).
> > --Eric
> > 
> > 	Eric Pettersen
> > 	USCF Computer Graphics Lab
> > 
> > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote:
> > 
> > > Hi:
> > > Is there a command in Chimera to protonate (Sybyl-type) the
> > > heteroatoms only (or deprotonate the other elements from a fully
> > > protonated protein)?
> > > thanks
> > > francesco pietra
> > > _______________________________________________
> > > Chimera-users mailing list
> > > Chimera-users at cgl.ucsf.edu
> > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > 
> > 
> > 
> > ------------------------------
> > 
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
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> > 
> > End of Chimera-users Digest, Vol 73, Issue 11
> > *********************************************
> > 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 12 May 2009 08:39:11 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] adding pseudo bonds
> To: JeanDidier.Marechal at uab.es
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <06B51782-B5EB-487A-B770-ACA04AA2D738 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Hi JD,
> The "user interface" (i.e. no programming) way is to create a text  
> file listing the desired pseudobonds and their colors and read it 
> in  
> with PseudoBond Reader.  The tool and file format are described here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html 
> >
> 
> I don't know the python way, but perhaps looking in the code for  
> PseudoBond Reader will help ( share/PBReader/ within your Chimera  
> installation).
> Best,
> 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 12, 2009, at 8:19 AM, Jean Didier Pie Marechal wrote:
> 
> > Dear all,
> >
> > what is the way to add pseubond between metal and chelating atoms?
> > if you could tell me what are the "mouse driven" and "script 
> driven"  
> > manner I'll be very pleased....
> > all the best,
> > JD
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> 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 13
> *********************************************
> 