[chimera-dev] Suggestion - notebook?

Thu Nov 13 01:24:35 PST 2008

Dear all,

I have no idea how complicated that would be and I don’t want to increase
your todo list, but I wonder if you could add a text entry in the chimera
.py file that you could acces through an editor window (integrated in
chimera would be perfect). I would find such thing extremely useful.

Best,

JD

De: Jean-Didier Maréchal [mailto:jeandidier.marechal at gmail.com] 
Enviado el: jueves, 13 de noviembre de 2008 9:23
Para: Eric Pettersen
CC: chimera-dev at cgl.ucsf.edu
Asunto: Re: [chimera-dev] python equivalent for Axis

Hi Eric, 
thanks a lot for this that's just perfect! 

I'm afraid that I have another question. Could you tell me what is the
easiest way to rotate only one model or a given selection of a model around
an axis passing through its center of rotation?

What I am trying to do is to rotate only one model (or a subset of one model
:a water molecule,  a ligand etc..) around one of these calculated axis.
Basically, I am trying to pilot in my script a similar thing that the
"movement--> movement mouse mode" does with the "move selection mode". I
thought I had clear in mind how of deal with Xform, but I can't get work and
get mixed up. I looked at the MoveSelection scripts for inspiring me but I
get stuck. 

Thanks for any help

JD

2008/11/10 Eric Pettersen <pett at cgl.ucsf.edu>

Hi JD,
       The StructMeasure.bestLine routine almost does what you want, but
although it returns the eigenvectors, it doesn't return the eigenvalues (!)
which makes it kind of useless.  I'll be fixing that in tonight's build.  At
any rate, you can just conscript the underlying code:  if your list of atoms
is in the variable "atoms", then this will get you the eigenvectors/values:

       coords = chimera.numpyArrayFromAtoms(atoms)
       centroid = coords.mean(0)
       centered = coords - centroid
       from numpy.linalg import svd
       ignore, vals, vecs = svd(centered)

--Eric

On Nov 8, 2008, at 7:00 AM, Dr. Jean-Didier Maréchal wrote:

Dear all,

Sorry to bother you again with a similar kind of question, but I'd like my
script to stock in an array the three resulting vectors of the new
implemented calculation of the axes for a given set of selected atoms. The
truth is that I find the right python call for the axis function. I imported
StructMeasure and tried different ways around but I can't find my way
through. I don't know if I don't give the wrong arguments or have the wrong
syntaxes.

Thanks a lot for any help,

JD

-----Mensaje original-----
De: chimera-dev-bounces at cgl.ucsf.edu
[mailto:chimera-dev-bounces at cgl.ucsf.edu] En nombre de
chimera-dev-request at cgl.ucsf.edu
Enviado el: jueves, 06 de noviembre de 2008 21:00
Para: chimera-dev at cgl.ucsf.edu
Asunto: Chimera-dev Digest, Vol 58, Issue 2

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Today's Topics:

 1. atom spec. in BNF (David A. C. Beck)
 2. Re: atom spec. in BNF (Eric Pettersen)

----------------------------------------------------------------------

Message: 1
Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST)
From: "David A. C. Beck" <dacb at u.washington.edu>
Subject: [chimera-dev] atom spec. in BNF
To: chimera-dev at cgl.ucsf.edu
Message-ID:
       <Pine.LNX.4.64.0811051401230.9881 at homer23.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Does anyone have BNF notation for the atom specification 'language' used
by Chimera?  Thanks,
 - David

--
David A. C. Beck, Ph.D.
dacb at u.washington.edu
Valerie Daggett Laboratory
University of Washington, Seattle

------------------------------

Message: 2
Date: Wed, 5 Nov 2008 14:26:16 -0800
From: Eric Pettersen <pett at cgl.ucsf.edu>
Subject: Re: [chimera-dev] atom spec. in BNF
To: "David A. C. Beck" <dacb at u.washington.edu>
Cc: chimera-dev at cgl.ucsf.edu
Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D at cgl.ucsf.edu>
Content-Type: text/plain; charset="us-ascii"

On Nov 5, 2008, at 2:03 PM, David A. C. Beck wrote:

Does anyone have BNF notation for the atom specification 'language'
used
by Chimera?

I don't think so.  What's the use case here?  If you're in the context
of Chimera, you should be able to use Chimera's own atom-spec parsing
facilities, e.g. chimera.specifier.evalSpec().  Outside of Chimera,
I'm aware of a pretty extensive but not totally complete parser in
perl:  Chemistry::MidasPattern - Select atoms in macromolecules -
search.cpan.org

--Eric

                       Eric Pettersen
                       UCSF Computer Graphics Lab
                       http://www.cgl.ucsf.edu

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