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@uab.es----- Missatge original -----
De:
chimera-dev-request@cgl.ucsf.eduData: Dilluns, Novembre 23, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 70, Issue 2
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Today's Topics:
1. Rotation about the axis of symmetry (Liam Browne)
2. Re: Rotation about the axis of symmetry (Elaine Meng)
--------------------------------------------------------------------
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Message: 1
Date: Mon, 23 Nov 2009 10:06:26 +0000
From: Liam Browne <liam.browne@hotmail.co.uk>
To: <chimera-dev@cgl.ucsf.edu>
Subject: [chimera-dev] Rotation about the axis of symmetry
Message-ID: <COL124-W33C2F39CCE1734F40BEB30B69E0@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@cgl.ucsf.edu>
To: Liam Browne <liam.browne@hotmail.co.uk>
Cc: chimera-dev@cgl.ucsf.edu, "chimera-users@cgl.ucsf.edu BB"
<chimera-users@cgl.ucsf.edu>
Subject: Re: [chimera-dev] Rotation about the axis of symmetry
Message-ID: <4DA8829B-1427-4C99-B169-CB417166F35F@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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