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,

De: Jean-Didier Maréchal [mailto:jeandidier.marechal@gmail.com]
Enviado el: jueves, 13 de noviembre de 2008 9:23
Para: Eric Pettersen
CC: chimera-dev@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@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@cgl.ucsf.edu
[mailto:chimera-dev-bounces@cgl.ucsf.edu] En nombre de
chimera-dev-request@cgl.ucsf.edu
Enviado el: jueves, 06 de noviembre de 2008 21:00
Para: chimera-dev@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@u.washington.edu>
Subject: [chimera-dev] atom spec. in BNF
To: chimera-dev@cgl.ucsf.edu
Message-ID:
<Pine.LNX.4.64.0811051401230.9881@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@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@cgl.ucsf.edu>
Subject: Re: [chimera-dev] atom spec. in BNF
To: "David A. C. Beck" <dacb@u.washington.edu>
Cc: chimera-dev@cgl.ucsf.edu
Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D@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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