[chimera-dev] python equivalent for Axis
Tom Goddard
goddard at cgl.ucsf.edu
Thu Nov 13 12:47:59 PST 2008
Hi JD,
In Chimera 1.4 daily builds (not release candidate) the "turn" command
has been upgraded to allow rotating whole models about an arbitrary axis
and center:
turn 0.8,0.5,0.1 35 center 10,15,20 coordinateSystem #0 models #0
This turns model 0 by 35 degrees around the center point and axis
(0.8,0.5,0.1) specified in model #0 coordinates.
The turn command can't move a subset of atoms in a model. It just
changes the overall model transform. To move a few atoms you need to
change atom coordinates as is done by MoveSelection. I've attached a
bit of Python code as an example. Getting the transforms right is tricky.
Tom
Jean-Didier Maréchal wrote:
> 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 <mailto: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>
> [mailto: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
> <mailto:chimera-dev-request at cgl.ucsf.edu>
> Enviado el: jueves, 06 de noviembre de 2008 21:00
> Para: chimera-dev at cgl.ucsf.edu <mailto:chimera-dev at cgl.ucsf.edu>
> Asunto: Chimera-dev Digest, Vol 58, Issue 2
>
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> Today's Topics:
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> 1. atom spec. in BNF (David A. C. Beck)
> 2. Re: atom spec. in BNF (Eric Pettersen)
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>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST)
> From: "David A. C. Beck" <dacb at u.washington.edu
> <mailto:dacb at u.washington.edu>>
> Subject: [chimera-dev] atom spec. in BNF
> To: chimera-dev at cgl.ucsf.edu <mailto:chimera-dev at cgl.ucsf.edu>
> Message-ID:
>
> <Pine.LNX.4.64.0811051401230.9881 at homer23.u.washington.edu
> <mailto: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 <mailto: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
> <mailto:pett at cgl.ucsf.edu>>
> Subject: Re: [chimera-dev] atom spec. in BNF
> To: "David A. C. Beck" <dacb at u.washington.edu
> <mailto:dacb at u.washington.edu>>
> Cc: chimera-dev at cgl.ucsf.edu <mailto:chimera-dev at cgl.ucsf.edu>
> Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D at cgl.ucsf.edu
> <mailto: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 <http://search.cpan.org>
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
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