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@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimarts, Maig 12, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 13
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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)
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Message: 1 Date: Mon, 11 May 2009 14:32:22 -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.4.63.0905111420070.1959390@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@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@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
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Message: 2 Date: Tue, 12 May 2009 17:19:46 +0200 From: Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> Subject: [Chimera-users] adding pseudo bonds To: chimera-users@cgl.ucsf.edu Message-ID: <165553c1104b.4a09afb2@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@uab.es
----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Diumenge, Maig 10, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 11
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1. Protonate heteroatoms only (Francesco Pietra) 2. Re: Protonate heteroatoms only (Eric Pettersen)
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Message: 1 Date: Sat, 9 May 2009 23:35:37 +0200 From: Francesco Pietra <chiendarret@gmail.com> Subject: [Chimera-users] Protonate heteroatoms only To: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <b87c422a0905091435q4a1671e2td61284cf092e7fb6@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
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Message: 2 Date: Sat, 9 May 2009 15:27:55 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] Protonate heteroatoms only To: Francesco Pietra <chiendarret@gmail.com> Cc: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 3 Date: Tue, 12 May 2009 08:39:11 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] adding pseudo bonds To: JeanDidier.Marechal@uab.es Cc: chimera-users@cgl.ucsf.edu Message-ID: <06B51782-B5EB-487A-B770-ACA04AA2D738@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.h...
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@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
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