<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yuzheng,<div class=""><br class=""></div><div class=""> First I advise you to use ChimeraX which is the new version of Chimera. We have not developed Chimera for the last 6 years so it is best to use the new program if you are not yet tied to the old one.</div><div class=""><br class=""></div><div class=""> The description of the virus coordinate system transform is not clear. I see that supplementary figure S4 of the paper you cite has a similar unclear explanation (shown below). It would probably take reading the paper to understand what they did well enough to understand the coordinate transformation. If you have read it and can explain it clearly then I could advise on how to do it in ChimeraX.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.6b10131" class="">https://pubs.acs.org/doi/10.1021/acs.jpcb.6b10131</a></div><div class=""><br class=""></div><div class=""><img id="<9B75729B-10F4-4B56-A081-74BFA623D897>" alt="Screen Shot 2022-10-18 at 8.10.22 AM.png" apple-inline="yes" class="Apple-web-attachment" style="opacity: 1;" width="819" height="443" src="cid:9B75729B-10F4-4B56-A081-74BFA623D897"></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 18, 2022, at 7:44 AM, Feng, Y. via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi there,<br class=""><br class="">I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the Figure S4 of the following article: DOI: 10.1021/acs.jpcb.6b10131.<br class=""><br class="">My questions would be:<br class="">In Chimera,<br class="">1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)?<br class="">2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point?<br class=""><br class="">What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful.<br class=""><br class="">Sincerely appreciate!<br class=""><br class="">With best regards,<br class="">Yuzhen Feng<br class=""></div>
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