[chimera-dev] Adding atom types in the Gaff parameter files of chimera.
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Tue Jul 13 02:21:21 PDT 2010
I am trying to add another type of atom in the GAFF parameter file that is called during the minimization process and can't find the right place.
Could you give me a hand please?
Dr. Jean-Didier Maréchal
The Computational Biotechnological Chemistry Team
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
08193 Cerdanyola (Barcelona)
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dimecres, Juny 30, 2010 9:00 pm
Assumpte: Chimera-dev Digest, Vol 76, Issue 4
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> Today's Topics:
> 1. Re: pil background Image (Greg Couch)
> Message: 1
> Date: Tue, 29 Jun 2010 14:10:46 -0700
> From: Greg Couch <postmaster at cgl.ucsf.edu>
> To: Ludovic Autin <autin at scripps.edu>
> Cc: "chimera-dev at cgl.ucsf.edu" <chimera-dev at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] pil background Image
> Message-ID: <4C2A6156.6070100 at cgl.ucsf.edu>
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> Hi Ludovic,
> This is possible, but a little tricky. It requires writing Python
> code. So if I were to code a solution (and I may if you don't, but
> need to fix a few bugs first), I'd make a chimera extension that
> load an image into an OpenGL texture, then in the 2D drawing pass,
> draw it underneath everything that is currently drawn. The reason
> using a texture instead of a bitmap is to allow for high resolution
> backgrounds for saving images.
> If you are inclined to write this yourself, code for a chimera
> that does OpenGL in Python can be found in the CHIMERA/share/Ilabel
> -- Greg
> On 6/23/2010 2:14 PM, Eric Pettersen wrote:
> > On Jun 22, 2010, at 1:25 PM, Ludovic Autin wrote:
> >> Hi,
> >> I would like to know if its possible to use a PIL or a raw image
> as a
> >> background image.
> >> And/Or can you help me figure out how to do it (maybe using some
> >> volume from image functinoality).
> >> Ideally, I would like to be able to update in realtime this
> >> background image (either using a thread, or a callback)
> > Hi Ludovic,
> > The developer who could authoritatively answer your question
> > Couch) is out this week, so I'll take a stab at it: I don't
> think so.
> > :-) However, if your goal is to, say, make a movie with a
> > you provide then you could write out image files with a
> > background (described in this message:
> > http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-
> > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-
> > and use most any image-processing program to compose the Chimera
> > images with the background(s) you prefer.
> > Despite my flippant answer in the first sentence, I don't really
> > if it is possible to directly change the background. When Greg
> > back I hope he will comment on that. Perhaps you could say more
> > what your ultimate goal is?
> > --Eric
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> > http://www.cgl.ucsf.edu
> Hi Ludovic,
> Everything is possible.
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