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 Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..." 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
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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When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..."
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
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
Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..."
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
Dear all, I have no idea how complicated that would be and I dont 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, JD 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 Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..." 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
On Nov 13, 2008, at 1:24 AM, Dr. Jean-Didier Maréchal wrote:
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.
Hi JD, So what you're asking for is some kind of tool where you can type in notes, and that would be preserved through sessions? Is that right? We were already planning to allow model renaming and the adding of short notes for each model, but this sounds like a nice supplement to that. Consider my to-do list increased. :-) --Eric
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
Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu>
To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu <mailto:chimera-dev-request@cgl.ucsf.edu>
You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu <mailto:chimera-dev-owner@cgl.ucsf.edu>
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..."
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 <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
------------------------------
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()))
participants (4)
-
Dr. Jean-Didier Maréchal -
Eric Pettersen -
Jean-Didier Maréchal
-
Tom Goddard