<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="">That is correct.<div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 14, 2022, at 6:31 AM, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thank you for your reply. I have one question to make sure I understand correctly. *1.5 expands them by 50%, so say I only wanted to do 25% I would use *1.25 to expand? I do appreciate this. <div class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class="">Thank you,</div><div class=""><br class=""></div><div class="">Heather Noriega</div>PhD-Pharmaceutical Science student <div class="">Howard University<br class=""><div class=""><a href="mailto:heather.noriega@bison.howard.edu" target="_blank" class="">heather.noriega@bison.howard.edu</a></div><div class="">520-203-1883</div></div></div></div></div><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 10, 2022 at 7:37 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">If you just want to do that unphysical stretching, open the Python Shell tool (Tools→General→Shell) and type:<div class=""><br class=""></div><div class="">from chimerax.atomic import all_atoms</div><div class="">atoms = all_atoms(session)</div><div class="">atoms.coords = atoms.coords * 1.5</div><div class=""><br class=""></div><div class="">… to expand the coordinates by 50%.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Nov 9, 2022, at 6:49 PM, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">Yes, it does make it arbitrary. The picture was from another study, not the family I am working on. It was a request from a colleague, I was just seeing if there was an easy way of doing it, instead of manually. Thank you though. I hope you have a good evening.</div><div class=""><br clear="all" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Thank you,</div><div class=""><br class=""></div><div class="">Heather Noriega</div>PhD-Pharmaceutical Science student <div class="">Howard University<br class=""><div class=""><a href="mailto:heather.noriega@bison.howard.edu" target="_blank" class="">heather.noriega@bison.howard.edu</a></div><div class="">520-203-1883</div></div></div></div></div><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 9, 2022 at 9:34 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Heather,<br class="">
Sorry, there isn't a feature like that. You could imagine expanding all the atomic XYZ coordinates radially from the protomer center but in my opinion it would make the structure ridiculous (unphysical bond lengths etc.)... and even if you wanted to do that, as far as I know you would have to write your own code to do it. The picture suggests there is already a structure of the bigger one, however.<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="">
> On Nov 9, 2022, at 6:19 PM, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
> <br class="">
> Hello,<br class="">
> <br class="">
> I hope this email finds everyone well. I was wondering if ChimeraX had a function specific to "stretching" the protein. I am going to attach a picture, for reference. Is it possible to stretch the monomer to build a larger capsid? Thanks in advance.<br class="">
> <br class="">
> Thank you,<br class="">
> <br class="">
> Heather Noriega<br class="">
> PhD-Pharmaceutical Science student <br class="">
> Howard University<br class="">
> <a href="mailto:heather.noriega@bison.howard.edu" target="_blank" class="">heather.noriega@bison.howard.edu</a><br class="">
> 520-203-1883<br class="">
> <image.png><br class="">
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