[chimera-dev] Adding atom types in the Gaff parameter files of chimera.

[Jean Didier Pie Marechal]

HI guys,

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?

best,
JD


Dr. Jean-Didier Maréchal
Lecturer
The Computational Biotechnological Chemistry Team
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
www: http://asklipio.qf.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:
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>   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>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> 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 
> I 
> need to fix a few bugs first), I'd make a chimera extension that 
> would 
> load an image into an OpenGL texture, then in the 2D drawing pass, 
> I'd 
> draw it underneath everything that is currently drawn.  The reason 
> for 
> 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 
> extension 
> that does OpenGL in Python can be found in the CHIMERA/share/Ilabel 
> package.
> 
>     -- 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 
> (Greg 
> > 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 
> background 
> > you provide then you could write out image files with a 
> transparent 
> > background (described in this message: 
> > http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-
> January/002197.html) 
> > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-
> January/002197.html%29> 
> > 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 
> know 
> > if it is possible to directly change the background.  When Greg 
> gets 
> > back I hope he will comment on that.  Perhaps you could say more 
> about 
> > 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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