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@uab.es
----- Missatge original ----- De: chimera-dev-request@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)
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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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