Adding atom types in the Gaff parameter files of chimera.

13 Jul 2010


      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@uab.es
www: http://asklipio.qf.uab.es
----- Missatge original -----
De: chimera-dev-request@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:

Re: pil background Image (Greg Couch)


--
Message: 1
Date: Tue, 29 Jun 2010 14:10:46 -0700
From: Greg Couch postmaster@cgl.ucsf.edu
To: Ludovic Autin autin@scripps.edu
Cc: "chimera-dev@cgl.ucsf.edu" chimera-dev@cgl.ucsf.edu
Subject: Re: [chimera-dev] pil background Image
Message-ID: 4C2A6156.6070100@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.

Jean Didier Pie Marechal

Eric Pettersen

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