[chimera-dev] scripting rotation around a bond

Wed Apr 29 03:34:22 PDT 2009

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 at uab.es

----- Missatge original -----
De: chimera-dev-request at 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)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Fri, 24 Apr 2009 13:45:42 -0400
> From: Randy Heiland <heiland at indiana.edu>
> Subject: Re: [chimera-dev] stereo: Linux, nvidia Quadro FX 5600
> To: Greg Couch <gregc at cgl.ucsf.edu>
> Cc: "chimera-dev at cgl.ucsf.edu" <chimera-dev at cgl.ucsf.edu>
> Message-ID: <9CE3734E-31AE-45C3-B5DC-80BC2D67856C at 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 at reald.com
> > www.reald.com
> >
> >
> >
> >
> > -----Original Message-----
> > From: Randy Heiland [heiland at 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
> >>
> >> _______________________________________________
> >> Chimera-dev mailing list
> >> Chimera-dev at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> >>
> 
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