<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="">Hi Elaine,<div class=""><br class=""></div><div class="">Yes, that helped immensely! I managed to untwist one strand of a 10bp DNA model using a combination of “torsion” and “angle”. I then opened the same model and the two did morph but not with an untwisting motion. </div><div class=""><br class=""></div><div class="">There’s no option to make untwisted DNA with a straight backbone in Avogadro so I’ll experiment with “angle”, “torsion” and “move”. I will let you know how I go.</div><div class=""><br class=""></div><div class="">Many thanks for your advice,</div><div class=""><br class=""></div><div class="">Ruben</div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On 23 Feb 2021, at 2:37 am, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><blockquote type="cite" class="">On Feb 21, 2021, at 11:40 PM, Ruben Meerman <<a href="mailto:rubenmeerman@me.com" class="">rubenmeerman@me.com</a>> wrote:<br class=""><br class="">I am trying to use the move command to move all the atoms of a single DNA nucleotide, but the whole model moves:<br class=""><br class="">move x 3 5 model #1 atoms #1/a:44<br class=""><br class="">The PDB model I’m testing the command on is 6BY7 (a DNA nano barrel) <br class=""><br class="">Am I doing something wrong, or just dopey?<br class="">Kind regards,<br class="">Ruben<br class=""><br class="">ps my ultimate aim is to a set of commands to untwist and unzip DNA using the move and roll commands… not sure if that’s a bit too ambitious<br class=""></blockquote><br class="">Hi Ruben,<br class="">I'm CC-ing the list, but yes in general please do send the question to the list in the first place unless it includes data that you have to keep private.<br class=""><br class="">The "model #1" option says to move all of model #1. Omit that if you only want to move the atoms. Also it looks like you have an extra number in there (3 or the 5). Maybe something like:<br class=""><br class="">move x 5 atoms #1/A:44<br class=""><br class="">"move" manual page:<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html</a>><br class=""><br class="">Structure 6by7 does not have a chain A, so you'd need a different command than the above for that specific structure.<br class=""><br class="">However, it sounds very difficult to untwist DNA using rigid-body movements of sets of atoms. Here are a couple of other ideas, but they are just ideas (don't know whether either one would work well) and would also take some effort to try.<br class=""><br class="">(1) use "torsion" command instead<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html</a>><br class=""><br class="">(2) build a separate completely untwisted version (not available in ChimeraX, maybe via other programs, or in ChimeraX by using "torsion") and then use "morph" to morph between the twisted and untwisted<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><br class=""><br class=""></div></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px; -webkit-text-decorations-in-effect: none;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">______________________</div><div class=""><div apple-content-edited="true" class=""><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><div class="">Ruben Meerman</div><div class=""><font color="#00a3d7" class="">M:</font> 0414 680 271</div><div class=""><font color="#00a3d7" class="">E:</font> <a href="mailto:rubenmeerman@me.com" class="">rubenmeerman@me.com</a></div><div class=""><br class=""></div></span></div></div></div></span></div></div></div><br class="Apple-interchange-newline">
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