Dear all, I'd like to generate from my script an ensemble of structures obtained by the rotation of a subgroup of the molecule around a given bond. Said in another way, I want to do something similar to the adjust torsion tools without getting to the interfase but defining myself the value of the angle I want to test. I can't figure out what is the module to load and how to use it and it seems there is no command line for this (rotation seems to accept only the atom specification for the bond as an argument). Could you give me a hand on this? By the way, I wanted to get the to the programmers's guide but I can't. You removed it from your server correct? All the 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-dev-request@cgl.ucsf.edu Data: Divendres, Abril 24, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 63, Issue 7
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Today's Topics:
1. Re: stereo: Linux, nvidia Quadro FX 5600 (Randy Heiland)
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Message: 1 Date: Fri, 24 Apr 2009 13:45:42 -0400 From: Randy Heiland <heiland@indiana.edu> Subject: Re: [chimera-dev] stereo: Linux, nvidia Quadro FX 5600 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: "chimera-dev@cgl.ucsf.edu" <chimera-dev@cgl.ucsf.edu> Message-ID: <9CE3734E-31AE-45C3-B5DC-80BC2D67856C@indiana.edu> Content-Type: text/plain; charset="us-ascii"
Just thought I'd add to this thread, in hopes that it may save others some time...
On Apr 24, 2009, at 11:22 AM, John Matthews wrote:
Hello Randy,
Unfortunately, the CE3s are not compatible with the new 120Hz LCDs from Viewsonic and Samsung. We are currently looking at a few possible solutions. When we have something, we'll post it on our website.
Thanks,
John Matthews | Sr. Engineer RealD 5335 Sterling Drive Boulder, CO 80301 (P) 303.545.5843 x121 | (F) 303.448.9573 | jmatthews@reald.com www.reald.com
-----Original Message----- From: Randy Heiland [heiland@indiana.edu] Sent: Friday, April 24, 2009 9:19 AM To: Real D Support Cc: Heiland Randy Subject: CrystalEyes and Viewsonic FuHzion
Hello,
I'd like to know if the CrystalEyes (CE-3) should work with the Viewsonic Fuhzion (120Hz) monitor? Just looking at the monitor thru them, it is very dark. Running glxgears in stereo does not work.
If they should indeed work, then perhaps I need a different nvidia driver.
Linux-x86_64 nvidia driver version: 180.29 GPU 0 (Quadro FX 5600)
thanks, Randy Heiland
On Apr 17, 2009, at 12:46 PM, Greg Couch wrote:
I don't remember how we configured our Linux machine for stereo, but the alternative to using the GUI to configure the X server for stereo, is to read the documentation that came with the NVidia driver in /usr/share/doc/NVIDIA_GLX-1.0/README.txt and configure xorg.conf with a text editor. Look in "Appendix D. X Config Options" for the "Stereo" and "AllowDFPStereo" options.
Good luck,
Greg
On Fri, 17 Apr 2009, Randy Heiland wrote:
Hello again gang,
I'm guessing someone there can help me get past this - I know Greg has offered advice elsewhere.
My subject line says it all - I want to get stereo working on this machine. Trying something more basic than chimera:
$ glxgears -stereo Error: couldn't get an RGB, Double-buffered, Stereo visual
$ glxinfo -v|grep stereo bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 ...
It's not obvious to me where/how one enables stereo via System-
Prefs- More Prefs->nvidia x server settings
The specs: Linux-x86_64 nvidia driver version: 180.29
GPU 0 (Quadro FX 5600) mem 1536 MB PCI Express 16x X screens: Screen 0 Display: Apple Cinema HDDisplay (DFP-1)
GPU 1 (Quadro NVS 290) 256 MB PCI Express 16x X screens: none Display: none
with an Apple 30" Cinema HDDisplay currently attached (and a ViewSonic Fuhzion, 120Hz as something else to experiment with). Currently have>> CrystalEyes.
I'd welcome any advice you might have. thanks, Randy
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On Apr 29, 2009, at 3:34 AM, Jean Didier Pie Marechal wrote:
Dear all,
I'd like to generate from my script an ensemble of structures obtained by the rotation of a subgroup of the molecule around a given bond. Said in another way, I want to do something similar to the adjust torsion tools without getting to the interfase but defining myself the value of the angle I want to test. I can't figure out what is the module to load and how to use it and it seems there is no command line for this (rotation seems to accept only the atom specification for the bond as an argument). Could you give me a hand on this?
Hi JD, Basically, given a bond you want to rotate around, you create a BondRot instance to do it: br = chimera.BondRot(bond) Then you can change it by a delta (in degrees) from it's _original_ (not current) position with the angle() method. You also have to specify which side of the bond doesn't move: br.angle = (10, br.biggerSide()) You can get back to the original position with br.reset() (or with a delta of zero). Make sure to dispose of the BondRot with br.destroy() when you're done with it. You probably want to use a daily build here, otherwise the bond- rotation GUI will pop up as you work with the BondRot. Which can be kind of cool as the adjustment dial flies around like a movie clock in a fast-forward sequence.
By the way, I wanted to get the to the programmers's guide but I can't. You removed it from your server correct?
All the best, JD
The Programmer's Guide is still there, it's just not a direct link off the home page. Instead you have to click on the "Documentation" link and it's in the list on the resulting page. We removed the auto- generated reference section since it was very big and of little utility. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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Jean Didier Pie Marechal