<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi JD,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Dec 3, 2009, at 7:24 AM, Jean Didier Pie Marechal wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>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. <br><br>All the best,<br>JD<br><br><br><br>Dr. Jean-Didier Maréchal<br>Lecturer<br>Computational Biotechnological Chemistry @ Transmet<br>Unitat de Química Física<br>Departament de Química<br>Universitat Autònoma de Barcelona<br>Edifici C.n.<br>08193 Cerdanyola (Barcelona)<br>Tel: +34.935814936<br>e-mail: <a href="mailto:JeanDidier.Marechal@uab.es">JeanDidier.Marechal@uab.es</a><br><br>----- Missatge original -----<br>De: <a href="mailto:chimera-dev-request@cgl.ucsf.edu">chimera-dev-request@cgl.ucsf.edu</a><br>Data: Dilluns, Novembre 23, 2009 9:00 pm<br>Assumpte: Chimera-dev Digest, Vol 70, Issue 2<br><br><blockquote type="cite">Send Chimera-dev mailing list submissions to<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:chimera-dev@cgl.ucsf.edu">chimera-dev@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">To subscribe or unsubscribe via the World Wide Web, visit<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a><br></blockquote><blockquote type="cite">or, via email, send a message with subject or body 'help' to<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:chimera-dev-request@cgl.ucsf.edu">chimera-dev-request@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You can reach the person managing the list at<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:chimera-dev-owner@cgl.ucsf.edu">chimera-dev-owner@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When replying, please edit your Subject line so it is more specific<br></blockquote><blockquote type="cite">than "Re: Contents of Chimera-dev digest..."<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Today's Topics:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> 1. Rotation about the axis of symmetry (Liam Browne)<br></blockquote><blockquote type="cite"> 2. Re: Rotation about the axis of symmetry (Elaine Meng)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--------------------------------------------------------------------<br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Message: 1<br></blockquote><blockquote type="cite">Date: Mon, 23 Nov 2009 10:06:26 +0000<br></blockquote><blockquote type="cite">From: Liam Browne <<a href="mailto:liam.browne@hotmail.co.uk">liam.browne@hotmail.co.uk</a>><br></blockquote><blockquote type="cite">To: <<a href="mailto:chimera-dev@cgl.ucsf.edu">chimera-dev@cgl.ucsf.edu</a>><br></blockquote><blockquote type="cite">Subject: [chimera-dev] Rotation about the axis of symmetry<br></blockquote><blockquote type="cite">Message-ID: <<a href="mailto:COL124-W33C2F39CCE1734F40BEB30B69E0@phx.gbl">COL124-W33C2F39CCE1734F40BEB30B69E0@phx.gbl</a>><br></blockquote><blockquote type="cite">Content-Type: text/plain; charset="iso-8859-1"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I want to rotate a model by 90 degrees about the axis of symmetry, <br></blockquote><blockquote type="cite">but I seem to be having problems setting the axis correctly.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">After two identical models are superimposed I use measure rotation <br></blockquote><blockquote type="cite">and get the following:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Matrix rotation and translation<br></blockquote><blockquote type="cite"> -0.04092271 -0.36724445 0.92922379 -82.20183653<br></blockquote><blockquote type="cite"> -0.91203666 0.39354649 0.11537022 -54.21831923<br></blockquote><blockquote type="cite"> -0.40806183 -0.84276490 -0.35104539 11.47082481<br></blockquote><blockquote type="cite"> Axis -0.55288898 0.77167664 -0.31437070<br></blockquote><blockquote type="cite"> Axis point -56.22800779 0.00000000 25.47389901<br></blockquote><blockquote type="cite"> Rotation angle (degrees) 119.94780111<br></blockquote><blockquote type="cite"> Shift along axis 0.00338820<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">What should I do to rotate the model at the same axis but by 90 <br></blockquote><blockquote type="cite">degrees?<br></blockquote><blockquote type="cite">Many thanks,<br></blockquote><blockquote type="cite">Liam<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_________________________________________________________________<br></blockquote><blockquote type="cite">View your other email accounts from your Hotmail inbox. Add them now.<br></blockquote><blockquote type="cite"><a href="http://clk.atdmt.com/UKM/go/186394592/direct/01/">http://clk.atdmt.com/UKM/go/186394592/direct/01/</a><br></blockquote><blockquote type="cite">-------------- next part --------------<br></blockquote><blockquote type="cite">An HTML attachment was scrubbed...<br></blockquote><blockquote type="cite">URL: <<a href="http://www.cgl.ucsf.edu/pipermail/chimera-">http://www.cgl.ucsf.edu/pipermail/chimera-</a><br></blockquote><blockquote type="cite">dev/attachments/20091123/dc41e16c/attachment-0001.html><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Message: 2<br></blockquote><blockquote type="cite">Date: Mon, 23 Nov 2009 09:26:17 -0800<br></blockquote><blockquote type="cite">From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br></blockquote><blockquote type="cite">To: Liam Browne <<a href="mailto:liam.browne@hotmail.co.uk">liam.browne@hotmail.co.uk</a>><br></blockquote><blockquote type="cite">Cc: <a href="mailto:chimera-dev@cgl.ucsf.edu">chimera-dev@cgl.ucsf.edu</a>,<span class="Apple-tab-span" style="white-space:pre"> </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB"<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br></blockquote><blockquote type="cite">Subject: Re: [chimera-dev] Rotation about the axis of symmetry<br></blockquote><blockquote type="cite">Message-ID: <<a href="mailto:4DA8829B-1427-4C99-B169-CB417166F35F@cgl.ucsf.edu">4DA8829B-1427-4C99-B169-CB417166F35F@cgl.ucsf.edu</a>><br></blockquote><blockquote type="cite">Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Nov 23, 2009, at 2:06 AM, Liam Browne wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">I want to rotate a model by 90 degrees about the axis of <br></blockquote></blockquote><blockquote type="cite">symmetry, <br></blockquote><blockquote type="cite"><blockquote type="cite">but I seem to be having problems setting the axis correctly.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">After two identical models are superimposed I use measure <br></blockquote></blockquote><blockquote type="cite">rotation <br></blockquote><blockquote type="cite"><blockquote type="cite">and get the following:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Matrix rotation and translation<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> -0.04092271 -0.36724445 0.92922379 -82.20183653<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> -0.91203666 0.39354649 0.11537022 -54.21831923<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> -0.40806183 -0.84276490 -0.35104539 11.47082481<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Axis -0.55288898 0.77167664 -0.31437070<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Axis point -56.22800779 0.00000000 25.47389901<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Rotation angle (degrees) 119.94780111<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Shift along axis 0.00338820<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">What should I do to rotate the model at the same axis but by 90 <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">degrees?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Many thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Liam<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Liam,<br></blockquote><blockquote type="cite">You can just use the reported values -- the tricky part is <br></blockquote><blockquote type="cite">remembering <br></blockquote><blockquote type="cite">to indicate that they are in the coordinate system of the first <br></blockquote><blockquote type="cite">model <br></blockquote><blockquote type="cite">in the "measure rotation" command, and also using the reported axis <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">point as the center of rotation.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Let's say you used the command "measure rotation #0 #1". Then the <br></blockquote><blockquote type="cite">values in the Reply Log are for the transformation of #1 relative <br></blockquote><blockquote type="cite">to <br></blockquote><blockquote type="cite">#0 expressed in the coordinate system of #0.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a> <br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Now you can use the values in the Reply Log to rotate #1 further. <br></blockquote><blockquote type="cite">Keep in mind that this transformation will be applied on top of any <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">existing transformations. If you want only the new rotation and <br></blockquote><blockquote type="cite">not <br></blockquote><blockquote type="cite">prior transformations, you would need to "reset default" first. To <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">rotate model #1 90 degrees about the reported axis and use the <br></blockquote><blockquote type="cite">reported axis point as the center, the command would be:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> turn -.55288898,.77167664,-.31437070 90 center <br></blockquote><blockquote type="cite">-56.22800779,0,25.47389901 mod #1 coord #0<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html</a>><br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D.<br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-dev mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">End of Chimera-dev Digest, Vol 70, Issue 2<br></blockquote><blockquote type="cite">******************************************<br></blockquote><blockquote type="cite"><br></blockquote><br>_______________________________________________<br>Chimera-dev mailing list<br><a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br></div></blockquote></div><br></div></body></html>