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@cgl.ucsf.edu <mailto: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> [mailto:chimera-dev-bounces@cgl.ucsf.edu <mailto:chimera-dev-bounces@cgl.ucsf.edu>] En nombre de chimera-dev-request@cgl.ucsf.edu <mailto:chimera-dev-request@cgl.ucsf.edu> Enviado el: jueves, 06 de noviembre de 2008 21:00 Para: chimera-dev@cgl.ucsf.edu <mailto: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)
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Message: 1 Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST) From: "David A. C. Beck" <dacb@u.washington.edu <mailto:dacb@u.washington.edu>> Subject: [chimera-dev] atom spec. in BNF To: chimera-dev@cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> Message-ID:
<Pine.LNX.4.64.0811051401230.9881@homer23.u.washington.edu <mailto: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 <mailto:dacb@u.washington.edu> Valerie Daggett Laboratory University of Washington, Seattle
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Message: 2 Date: Wed, 5 Nov 2008 14:26:16 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Subject: Re: [chimera-dev] atom spec. in BNF To: "David A. C. Beck" <dacb@u.washington.edu <mailto:dacb@u.washington.edu>> Cc: chimera-dev@cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D@cgl.ucsf.edu <mailto: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 <http://search.cpan.org>
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
# Rotate selected atoms using a given center, axis, and angle. from chimera import Point, Vector, Xform, selection center = Vector(10,15,20) axis = Vector(0.8,0.5,0.1) angle = 35 xf = Xform() xf.premultiply(Xform.translation(-center)) xf.premultiply(Xform.rotation(axis, angle)) xf.premultiply(Xform.translation(center)) atoms = selection.currentAtoms() for a in atoms: a.setCoord(xf.apply(a.coord()))