[chimera-dev] python equivalent for Axis

Thu Nov 13 00:23:16 PST 2008

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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