<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Jhanvi,<div><br></div><div> I made another virus morph movie, this time showing proteins as surfaces instead of ribbons using the command “sym #2 surf true res 3”.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/p22morph/p22surf.mp4">http://www.cgl.ucsf.edu/chimera/data/p22morph/p22surf.mp4</a></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/p22morph/p22surf.cmd">http://www.cgl.ucsf.edu/chimera/data/p22morph/p22surf.cmd</a></div><div><br></div><div>You need tomorrow’s Chimera daily build or release candidate (dated Nov 5, 2014 or later) to run this script since there was a Chimera bug that I fixed that caused repeated use of the sym command to consume all your memory.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><div><div>On Nov 3, 2014, at 5:52 PM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Jhanvi,<div><br></div><div> The idea is to morph the asymmetric units then copy the morph coordinates at each frame to the 59 other asymmetric units that make up the virus capsid. This uses commands sym (make asym unit copies), morph (compute the morph), coordset (play the morph), mcopy (copy coordinates), perframe (copy for each frame of morph), movie (record the movie). Here’s a movie showing P22 2xyy morphing to 2xyz and the script used to record it.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/p22morph/p22morph.mp4">http://www.cgl.ucsf.edu/chimera/data/p22morph/p22morph.mp4</a></div><div><br></div><div><span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/p22morph/p22morph.cmd">http://www.cgl.ucsf.edu/chimera/data/p22morph/p22morph.cmd</a></div><div><br></div><div>This used about 2.5 Gbytes of memory and about 20 minutes to render. You should use 64-bit Chimera to handle such big models. This example gives a poor result — ribbons show too much detail to see anything, coloring is atrocious. I tweaked the movie above putting a back clip plane to hide the back half of the virus. Normally I don’t do the full movie record in one command script. Instead I set of the scene, morphs, colors, molecule styles, clipping all using the normal Chimera user interface, then just do the movie record part with a script. I also save a session containing the setup scene in case I want to revise the movie later. It will be a big session file in this case because it contains the full virus capsid and large morph trajectory.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><div># Open P22 virus asymmetric unit</div><div>open 2xyy</div><div><br></div><div># Create full capsid</div><div>sym #0</div><div><br></div><div># Zoom to show full capsid</div><div>windowsize 800 800</div><div>focus</div><div><br></div><div># Open second state of P22.</div><div>open 2xyz</div><div><br></div><div># Compute morph from first state to second</div><div>morph start #0 frames 120</div><div>morph interpolate #2</div><div>morph movie</div><div><br></div><div># Undisplay the asymmetric units</div><div>~modeldisp #0,2</div><div><br></div><div># Color chains</div><div>rainbow chain</div><div><br></div><div># Record movie playing morph of asym unit and copying coordinates to full capsid.</div><div>movie record supersample 3</div><div>coord #3 1,120 ; perframe "mcopy #3 #1 settings x" frames 120</div><div>wait 120</div><div>movie encode ~/Desktop/p22morph.mp4 quality higher</div><div><br></div></div><div><br></div><div><br></div><div><br><div><div>On Nov 2, 2014, at 11:22 AM, Jhanvi Sharma wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear all,<div><br></div><div>I have just started using chimera. I am trying to make a movie for P22 Virus capsid expansion. </div><div>I have made the movie for asymmetric unit morph changes using the 2XYY and 2XYZ pdb IDs. However, I am unable to do it on whole P22 capsid model.</div><div>Kindly suggest the protocol I should use to get the desired result. I have seen many such movies in the articles. I am trying to achieve the same. For movie reference I am sending the link for article. </div><div><br></div><div><a href="http://www.sciencedirect.com/science/article/pii/S1047847705002686">http://www.sciencedirect.com/science/article/pii/S1047847705002686</a>.<br></div><div><br></div><div>I will appreciate your help.</div><div><br></div><div>Thanks,</div><div>Best regards,</div><div>Jhanvi Sharma</div></div>
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