<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">In general, if the start and end conformations are exactly the same for part of a structure then it should not move at all in a morph. If they are slightly different then it should move only slightly. If you are getting a large motion between start and end conformations that are only slightly different then that sounds like a bug. You could provide start and end structures or a movie clip to show what you are talking about.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On May 6, 2020, at 4:40 PM, Nandish Kumar Khanra <<a href="mailto:nkk2001@med.cornell.edu" class="">nkk2001@med.cornell.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Hi Elaine,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks for your reply. I will try these.</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Best,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Nandish</div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 865.328125px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, May 6, 2020 7:36 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Nandish Kumar Khanra <<a href="mailto:nkk2001@med.cornell.edu" class="">nkk2001@med.cornell.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax</font><div class=""> </div></div><div class="BodyFragment" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><font size="2" class=""><span style="font-size: 11pt;" class=""><div class="PlainText">Hi Nandish,<span class="Apple-converted-space"> </span><br class="">Not specifically, but you can try changing morph parameter options and values to see how they affect the intermediate conformations. I'd probably try changing the coreFraction and/or using "cartesian true" first, but it's not easy to predict what will help. Trial and error!<br class=""><br class=""><<a href="" class=""></a><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_morph.html-23morph-2Dparameters&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=zneLE2JksDxJlyvO8HmQxODwC4bbvOCqNarwuEW7-9M&s=nyr2pERHJ-WsBCTGQXM0bsZ87CAEQckfGuvuylF9NdM&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_morph.html-23morph-2Dparameters&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=zneLE2JksDxJlyvO8HmQxODwC4bbvOCqNarwuEW7-9M&s=nyr2pERHJ-WsBCTGQXM0bsZ87CAEQckfGuvuylF9NdM&e=</a><span class="Apple-converted-space"> </span>><br class=""><br class="">Elaine<br class=""><br class="">> On May 6, 2020, at 4:27 PM, Nandish Kumar Khanra <<a href="mailto:nkk2001@med.cornell.edu" class="">nkk2001@med.cornell.edu</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hi Elaine,<br class="">><span class="Apple-converted-space"> </span><br class="">> Thanks for your reply and for pointing out the total number of frames in the trajectory. The first and the end frames are the same as the start and end structures. however, I see the movement of few helices in the intermediate frames but these helices should not move in the intermediate frames also. Do you know how to overcome this?<br class="">><span class="Apple-converted-space"> </span><br class="">> Thanks,<br class="">> Nandish<br class="">> From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">> Sent: Wednesday, May 6, 2020 6:55 PM<br class="">> To: Nandish Kumar Khanra <<a href="mailto:nkk2001@med.cornell.edu" class="">nkk2001@med.cornell.edu</a>><br class="">> Cc:<span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax<br class="">> <span class="Apple-converted-space"> </span><br class="">> Hi Nandish,<br class="">> This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation.<br class="">><span class="Apple-converted-space"> </span><br class="">> I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change.<br class="">> <<a href="" class=""></a><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_morph.html&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=UzqNkQ0gUpzC3j3hqnOIwM6xC4UtnM7kYZblwWB41sY&s=XpLfbzhdDHv9aF5gM_FQTQGBrm4hYzlNcauOMtIUFcg&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_morph.html&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=UzqNkQ0gUpzC3j3hqnOIwM6xC4UtnM7kYZblwWB41sY&s=XpLfbzhdDHv9aF5gM_FQTQGBrm4hYzlNcauOMtIUFcg&e=</a><span class="Apple-converted-space"> </span>><br class="">><span class="Apple-converted-space"> </span><br class="">> I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames.<br class="">><span class="Apple-converted-space"> </span><br class="">> So your wait 100 command only ensures the first 100 frames are in the movie, not all 101.<br class="">><span class="Apple-converted-space"> </span><br class="">> I hope this helps,<br class="">> Elaine<br class="">> -----<br class="">> Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br class="">> UCSF Chimera(X) team<br class="">> Department of Pharmaceutical Chemistry<br class="">> University of California, San Francisco<br class="">><span class="Apple-converted-space"> </span><br class="">> > On May 6, 2020, at 3:33 PM, Nandish Kumar Khanra <<a href="mailto:nkk2001@med.cornell.edu" class="">nkk2001@med.cornell.edu</a>> wrote:<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > Hello all,<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.<span class="Apple-converted-space"> </span><br class="">> ><span class="Apple-converted-space"> </span><br class="">> > • Aligned two models using matchmaker,<br class="">> > mm #1 to #2 pair ss ss false<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > • make morph<br class="">> > morph #1,2 frames 100 play false cartesian true<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > • make movie<br class="">> > movie record size 1000,1000<br class="">> > coordset #3<br class="">> > wait 100<br class="">> > movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > Thanks,<br class="">> > Nandish<br class="">><span class="Apple-converted-space"> </span><br class="">> _______________________________________________<br class="">> ChimeraX-users mailing list<br class="">><span class="Apple-converted-space"> </span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">> Manage subscription:<br class="">><span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=zneLE2JksDxJlyvO8HmQxODwC4bbvOCqNarwuEW7-9M&s=drd0qVHISjnCshGQ2E5iQE-0Q9naEqaFEUNWPXA0jzk&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwIFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=zneLE2JksDxJlyvO8HmQxODwC4bbvOCqNarwuEW7-9M&s=drd0qVHISjnCshGQ2E5iQE-0Q9naEqaFEUNWPXA0jzk&e=</a><span class="Apple-converted-space"> </span><br class=""><br class=""></div></span></font></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div></body></html>