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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dear all,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>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.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>JD<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>De:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Jean-Didier
Maréchal [mailto:jeandidier.marechal@gmail.com] <br>
<b>Enviado el:</b> jueves, 13 de noviembre de 2008 9:23<br>
<b>Para:</b> Eric Pettersen<br>
<b>CC:</b> chimera-dev@cgl.ucsf.edu<br>
<b>Asunto:</b> Re: [chimera-dev] python equivalent for Axis<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Hi Eric, <br>
thanks a lot for this that's just perfect! <br>
<br>
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?<br>
<br>
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. <br>
<br>
Thanks for any help<br>
<br>
JD<br>
<o:p></o:p></p>
<div>
<p class=MsoNormal>2008/11/10 Eric Pettersen <<a
href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>><o:p></o:p></p>
<p class=MsoNormal>Hi JD,<br>
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:<br>
<br>
coords = chimera.numpyArrayFromAtoms(atoms)<br>
centroid = coords.mean(0)<br>
centered = coords - centroid<br>
from numpy.linalg import svd<br>
ignore, vals, vecs = svd(centered)<br>
<span style='color:#888888'><br>
--Eric</span><o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><br>
<br>
On Nov 8, 2008, at 7:00 AM, Dr. Jean-Didier Maréchal wrote:<o:p></o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Dear all,<br>
<br>
Sorry to bother you again with a similar kind of question, but I'd like my<br>
script to stock in an array the three resulting vectors of the new<br>
implemented calculation of the axes for a given set of selected atoms. The<br>
truth is that I find the right python call for the axis function. I imported<br>
StructMeasure and tried different ways around but I can't find my way<br>
through. I don't know if I don't give the wrong arguments or have the wrong<br>
syntaxes.<br>
<br>
Thanks a lot for any help,<br>
<br>
JD<br>
<br>
<br>
-----Mensaje original-----<br>
De: <a href="mailto:chimera-dev-bounces@cgl.ucsf.edu" target="_blank">chimera-dev-bounces@cgl.ucsf.edu</a><br>
[mailto:<a href="mailto:chimera-dev-bounces@cgl.ucsf.edu" target="_blank">chimera-dev-bounces@cgl.ucsf.edu</a>]
En nombre de<br>
<a href="mailto:chimera-dev-request@cgl.ucsf.edu" target="_blank">chimera-dev-request@cgl.ucsf.edu</a><br>
Enviado el: jueves, 06 de noviembre de 2008 21:00<br>
Para: <a href="mailto:chimera-dev@cgl.ucsf.edu" target="_blank">chimera-dev@cgl.ucsf.edu</a><br>
Asunto: Chimera-dev Digest, Vol 58, Issue 2<br>
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Today's Topics:<br>
<br>
1. atom spec. in BNF (David A. C. Beck)<br>
2. Re: atom spec. in BNF (Eric Pettersen)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST)<br>
From: "David A. C. Beck" <<a href="mailto:dacb@u.washington.edu"
target="_blank">dacb@u.washington.edu</a>><br>
Subject: [chimera-dev] atom spec. in BNF<br>
To: <a href="mailto:chimera-dev@cgl.ucsf.edu" target="_blank">chimera-dev@cgl.ucsf.edu</a><br>
Message-ID:<br>
<<a
href="mailto:Pine.LNX.4.64.0811051401230.9881@homer23.u.washington.edu"
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Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed<br>
<br>
Does anyone have BNF notation for the atom specification 'language' used<br>
by Chimera? Thanks,<br>
- David<br>
<br>
--<br>
David A. C. Beck, Ph.D.<br>
<a href="mailto:dacb@u.washington.edu" target="_blank">dacb@u.washington.edu</a><br>
Valerie Daggett Laboratory<br>
University of Washington, Seattle<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 5 Nov 2008 14:26:16 -0800<br>
From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>><br>
Subject: Re: [chimera-dev] atom spec. in BNF<br>
To: "David A. C. Beck" <<a href="mailto:dacb@u.washington.edu"
target="_blank">dacb@u.washington.edu</a>><br>
Cc: <a href="mailto:chimera-dev@cgl.ucsf.edu" target="_blank">chimera-dev@cgl.ucsf.edu</a><br>
Message-ID: <<a
href="mailto:88F81EBE-CCD4-495F-9316-FEA5D095965D@cgl.ucsf.edu" target="_blank">88F81EBE-CCD4-495F-9316-FEA5D095965D@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
On Nov 5, 2008, at 2:03 PM, David A. C. Beck wrote:<o:p></o:p></p>
<p class=MsoNormal>Does anyone have BNF notation for the atom specification
'language'<br>
used<br>
by Chimera?<o:p></o:p></p>
<p class=MsoNormal><br>
I don't think so. What's the use case here? If you're in the
context<br>
of Chimera, you should be able to use Chimera's own atom-spec parsing<br>
facilities, e.g. chimera.specifier.evalSpec(). Outside of Chimera,<br>
I'm aware of a pretty extensive but not totally complete parser in<br>
perl: Chemistry::MidasPattern - Select atoms in macromolecules -<br>
<a href="http://search.cpan.org" target="_blank">search.cpan.org</a><br>
<br>
--Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<a href="http://www.cgl.ucsf.edu" target="_blank">http://www.cgl.ucsf.edu</a><br>
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