<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="">Another way to make the copies is to use the Chimera sym command. For example,<div class=""><br class=""></div><div class=""> sym #0 group shift,5,14 axis z</div><div class=""><br class=""></div><div class="">copies model #0 five times at 14 Angstrom spacing along the z axis of the model #0 coordinate system (not the view direction coordinate system).</div><div class=""><br class=""></div><div class=""> <a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</a></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=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 29, 2021, at 10:16 AM, Thirumurugan Prakasam 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=""><meta charset="UTF-8" class=""><div 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="">Thank you so much Elaine for your quick response and help.<div class="">Many Thanks,</div><div class="">Thiru</div></div><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=""><div class="gmail_quote" 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;"><div dir="ltr" class="gmail_attr">On Fri, Oct 29, 2021 at 8:40 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">Hi Thiru,<br class="">If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.<br class=""><br class="">E.g. if the starting structure is oriented exactly so that you can stack them in Z (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:<br class=""><br class="">open myfile.pdb<br class="">open myfile.pdb<br class="">open myfile.pdb<br class=""><br class="">... then you would have models #0,1,2. To stack (REMEMBER don't rotate the view by hand yet!):<br class=""><br class="">move z 35 model #1<br class="">move z 70 model #2<br class=""><br class="">If it were X or Y axis instead of Z, then you would use x or y in the command instead of z. If you mess up you can use command "reset" and then start over with the move commands.<br class=""><br class="">See "move" help:<br class=""><<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_move.html&d=DwIFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=W_iTL8zm-aasz2PWuQlh91HFZlluzIuOYNUkSse6VCg&s=hPTcvB8jZ7V052xezzJt_VpKl3mWKQVui_IsjGjRA_g&e=" rel="noreferrer" target="_blank" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_move.html&d=DwIFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=W_iTL8zm-aasz2PWuQlh91HFZlluzIuOYNUkSse6VCg&s=hPTcvB8jZ7V052xezzJt_VpKl3mWKQVui_IsjGjRA_g&e=</a><span class="Apple-converted-space"> </span>><br class=""><br class="">After you are done opening/stacking, then you can rotate the view by hand.<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="">> On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hi,<br class="">> I need help to stack the crystal structures stack on top of each other. For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera?<br class="">> <image.png><br class="">><span class="Apple-converted-space"> </span><br class="">> Thanks,<br class="">> Thiru<br class=""><br class=""></blockquote></div><br clear="all" 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 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=""><br class=""></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 class="Apple-converted-space"> </span></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=""><div dir="ltr" class="gmail_signature" 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;"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">Thirumurugan Prakasam,</span><br class=""><span style="color: rgb(51, 51, 255); font-family: verdana, sans-serif;" class="">Research Scientist,</span><br class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">New York University Abu Dhabi,</span><br class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">Experimental Research Building</span><br class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">Building C1, Saadiyat Island</span><br class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">Abu Dhabi, UAE</span></div><div dir="ltr" class=""><span style="font-family: verdana, sans-serif; color: rgb(51, 51, 255);" class="">Phone no: +971-561976358</span><div style="margin-bottom: 0.0001pt;" class=""><br class="webkit-block-placeholder"></div><p class=""><span style="font-family: serif, serif; color: rgb(51, 51, 255);" class=""> <br class=""></span></p></div></div></div></div></div></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; 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