<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 31, 2011, at 6:59 AM, Lukasz Walewski wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br><br>I am looking at the trajectory with thermal anisotropy factors that<br>change from frame to frame, i.e. I have a multi-frame PDB file that<br>contains ATOM and ANISOU records. The components of the anisotropy<br>tensors change during the simulation (the data I am analyzing has a<br>redefined meaning). I am able to properly read and play the trajectory.<br>Ellipsoid representation of the thermal U factors works excellent for a<br>single frame. However it seems that the ellipsoids are not updated when<br>I play the trajectory, i.e. the atoms move as expected but the<br>ellipsoids retain both their positions and shape from the first frame.<br>Is there any way around ?<br></div></blockquote><div><br></div>Hi Lukasz,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera doesn't store any info on a per-frame basis right now, so the shortest answer is no. However, depending on the size of the system you are working with and the length of your trajectory (and your patience!) there may be a workaround. Basically the workaround is to read your trajectory file using the regular FIle..Open dialog rather than with the trajectory tool. This will cause each MODEL in your file to be opened as a separate model in Chimera. This consumes a lot more memory than the trajectory would, so I would say it is practical if we are talking dozens of models or less, or hundreds of models if your system is no more than 1000 atoms or so, or a few thousand models if we're talking about a small molecule.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Of course you lose the convenience of the MD Movie's playback interface. Nonetheless, you can get a poor man's playback with a script like this:</div><div><br></div><div>aniso parameters-you-want</div><div>~modeldisp</div><div>modeldisp #0.1; some-timing-command</div><div>~modeldisp #0.1; modeldisp #0.2; some-timing-command</div><div>~modeldisp #0.2; modeldisp #0.3; some-timing-command</div><div>etc.</div><div><br></div><div>Hopefully you or someone you know is familiar with programming, which would allow you to create such a script easily rather than by insanely tedious hand editing. You run the script either with File...Open or the "open" command. The script file name should end in ".cmd" or ".com". </div><div><span class="Apple-tab-span" style="white-space:pre"> </span>A couple of points about the script:</div><div>1) Commands on the same line separated by semi-colons are executed without the screen being redrawn between commands.</div><div>2) There are a couple of choices for "some-timing-command":</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>a) "wait N" where N is an integer. In that case Chimera will wait that many thirtieths of a second before going on to the next command. So "wait 15" would pause half a second before going on to the next command. Keep in mind that as such a script runs it can be paused by pressing Shift-Esc (and then resumed the same way) or aborted by pressing Esc.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>b) "pause" which will suspend script execution until any key other than Esc or End is pressed. Pressing End will abort a "paused" script.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I will be opening a feature-request ticket in our bug database for storing some information on a per-frame basis and getting Thermal Ellipsoids to use it, with you on the recipient list so that you'll be notified when it gets worked on.</div><div><br></div><div><blockquote type="cite"><div>In any case I find Chimera wonderful software that I came upon only<br>recently. Thanks guys for developing it!</div></blockquote><br></div><div>Thanks! We're working on our NIH grant renewal right now. Hopefully that will translate into several more years of funding. Keep your fingers crossed!</div><div><br></div><div>--Eric</div><br><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></body></html>