[chimera-dev] MD movie for xyz format
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Thu Dec 3 07:24:40 PST 2009
Dear all,
would it be possible to have xyz format accepted for the MD movie tool. Someting identical to the PDB (with both multiple xyz file or unique xyz file containing several structures) would be more than enough. We frequently use this standard and that would be useful for us to have such possbility.
All the best,
JD
Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dilluns, Novembre 23, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 70, Issue 2
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> Today's Topics:
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> 1. Rotation about the axis of symmetry (Liam Browne)
> 2. Re: Rotation about the axis of symmetry (Elaine Meng)
>
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> --------------------------------------------------------------------
> --
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> Message: 1
> Date: Mon, 23 Nov 2009 10:06:26 +0000
> From: Liam Browne <liam.browne at hotmail.co.uk>
> To: <chimera-dev at cgl.ucsf.edu>
> Subject: [chimera-dev] Rotation about the axis of symmetry
> Message-ID: <COL124-W33C2F39CCE1734F40BEB30B69E0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi all,
>
> I want to rotate a model by 90 degrees about the axis of symmetry,
> but I seem to be having problems setting the axis correctly.
>
> After two identical models are superimposed I use measure rotation
> and get the following:
>
> Matrix rotation and translation
> -0.04092271 -0.36724445 0.92922379 -82.20183653
> -0.91203666 0.39354649 0.11537022 -54.21831923
> -0.40806183 -0.84276490 -0.35104539 11.47082481
> Axis -0.55288898 0.77167664 -0.31437070
> Axis point -56.22800779 0.00000000 25.47389901
> Rotation angle (degrees) 119.94780111
> Shift along axis 0.00338820
>
> What should I do to rotate the model at the same axis but by 90
> degrees?
> Many thanks,
> Liam
>
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> Message: 2
> Date: Mon, 23 Nov 2009 09:26:17 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Liam Browne <liam.browne at hotmail.co.uk>
> Cc: chimera-dev at cgl.ucsf.edu, "chimera-users at cgl.ucsf.edu BB"
> <chimera-users at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Rotation about the axis of symmetry
> Message-ID: <4DA8829B-1427-4C99-B169-CB417166F35F at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Nov 23, 2009, at 2:06 AM, Liam Browne wrote:
>
> > I want to rotate a model by 90 degrees about the axis of
> symmetry,
> > but I seem to be having problems setting the axis correctly.
> > After two identical models are superimposed I use measure
> rotation
> > and get the following:
> >
> > Matrix rotation and translation
> > -0.04092271 -0.36724445 0.92922379 -82.20183653
> > -0.91203666 0.39354649 0.11537022 -54.21831923
> > -0.40806183 -0.84276490 -0.35104539 11.47082481
> > Axis -0.55288898 0.77167664 -0.31437070
> > Axis point -56.22800779 0.00000000 25.47389901
> > Rotation angle (degrees) 119.94780111
> > Shift along axis 0.00338820
> >
> > What should I do to rotate the model at the same axis but by 90
> > degrees?
> >
> > Many thanks,
> > Liam
>
> Hi Liam,
> You can just use the reported values -- the tricky part is
> remembering
> to indicate that they are in the coordinate system of the first
> model
> in the "measure rotation" command, and also using the reported axis
>
> point as the center of rotation.
>
> Let's say you used the command "measure rotation #0 #1". Then the
> values in the Reply Log are for the transformation of #1 relative
> to
> #0 expressed in the coordinate system of #0.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation
> >
>
> Now you can use the values in the Reply Log to rotate #1 further.
> Keep in mind that this transformation will be applied on top of any
>
> existing transformations. If you want only the new rotation and
> not
> prior transformations, you would need to "reset default" first. To
>
> rotate model #1 90 degrees about the reported axis and use the
> reported axis point as the center, the command would be:
>
> turn -.55288898,.77167664,-.31437070 90 center
> -56.22800779,0,25.47389901 mod #1 coord #0
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
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