[chimera-dev] MD movie for xyz format
Eric Pettersen
pett at cgl.ucsf.edu
Thu Dec 3 14:21:11 PST 2009
Hi JD,
I put in support for XYZ trajectories in tomorrow's daily build. It
only supports multiple-file trajectories since Chimera's XYZ reader
doesn't support multiple molecules per file and there was only so much
effort I wanted to go to! I thought it would be a little easier than
it was because I thought it would basically be copying the PDB
trajectory code and hacking out the single-file trajectory stuff and
changing a bunch of "PDB"s to "XYZ"s. About half way through it
dawned on me that the multi-file PDB code relies on the C++ NMR-
ensemble reading code to read the files (it collates the individual
files into a single MODEL-separated file and hands that off to the C++
layer and out pops a Molecule with multiple coordinate sets). So I
had to add some code to read the XYZ files individually, get a
Molecule, and add the Molecule's coordinate set to the first
Molecule's coordinate set. Unfortunately there are no methods in the
Python layer for setting coordinate sets in bulk so the coordinates
are copied one at a time. So I don't know how fast the XYZ trajectory
will be in practice. Probably will be okay if your XYZ systems don't
have tons of atoms or don't have too many frames.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
On Dec 3, 2009, at 7:24 AM, Jean Didier Pie Marechal wrote:
> 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:
>>
>> 1. Rotation about the axis of symmetry (Liam Browne)
>> 2. Re: Rotation about the axis of symmetry (Elaine Meng)
>>
>>
>> --------------------------------------------------------------------
>> --
>>
>> 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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