<div dir="ltr">Thanks Tom for your suggestions.<div>Thanks,</div><div>Thiru</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Oct 29, 2021 at 10:06 PM Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:<br></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;">Another way to make the copies is to use the Chimera sym command.  For example,<div><br></div><div> sym #0 group shift,5,14 axis z</div><div><br></div><div>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><br></div><div>   <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_UsersGuide_midas_sym.html&d=DwMFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=I7qtfA8N7Q5sp4JqE2oPCZchG4tZN6Z7nJw71FRlb-o&s=EcVad0ZZtSpjfQ7zIJAUgEf2-0-pYw1_07oRMovpmWE&e=" target="_blank">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</a></div><div><br></div><div><span style="white-space:pre-wrap"> </span>Tom</div><div><br></div><div><br><div><br><blockquote type="cite"><div>On Oct 29, 2021, at 10:16 AM, Thirumurugan Prakasam via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br><div><div dir="ltr" style="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;text-decoration:none">Thank you so much Elaine for your quick response and help.<div>Many Thanks,</div><div>Thiru</div></div><br style="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;text-decoration:none"><div class="gmail_quote" style="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;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" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Thiru,<br>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><br>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><br>open myfile.pdb<br>open myfile.pdb<br>open myfile.pdb<br><br>... then you would have models #0,1,2.  To stack (REMEMBER don't rotate the view by hand yet!):<br><br>move z 35 model #1<br>move z 70 model #2<br><br>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><br>See "move" help:<br><<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">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> </span>><br><br>After you are done opening/stacking, then you can rotate the view by hand.<br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D.                       <br>UCSF Chimera(X) team<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><br>> On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>><span> </span><br>> Hi,<br>> 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>> <image.png><br>><span> </span><br>> Thanks,<br>> Thiru<br><br></blockquote></div><br clear="all" style="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;text-decoration:none"><div style="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;text-decoration:none"><br></div><span style="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;text-decoration:none;float:none;display:inline">--<span> </span></span><br style="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;text-decoration:none"><div dir="ltr" style="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;text-decoration:none"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Thirumurugan Prakasam,</span><br><span style="color:rgb(51,51,255);font-family:verdana,sans-serif">Research Scientist,</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">New York University Abu Dhabi,</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Experimental Research Building</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Building C1, Saadiyat Island</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Abu Dhabi, UAE</span></div><div dir="ltr"><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Phone no: +971-561976358</span><div style="margin-bottom:0.0001pt"><br></div><p><span style="font-family:serif,serif;color:rgb(51,51,255)"> <br></span></p></div></div></div></div></div></div><span style="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;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="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;text-decoration:none"><span style="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;text-decoration:none;float:none;display:inline">Chimera-users mailing list:<span> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="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" target="_blank">Chimera-users@cgl.ucsf.edu</a><br style="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;text-decoration:none"><span style="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;text-decoration:none;float:none;display:inline">Manage subscription:<span> </span></span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwMFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=I7qtfA8N7Q5sp4JqE2oPCZchG4tZN6Z7nJw71FRlb-o&s=q4PBxPGDg83xCyV3ZWNc5I0yR7DbjLRGf38bD3ThkAs&e=" style="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" target="_blank">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Thirumurugan Prakasam,</span><br><span style="color:rgb(51,51,255);font-family:verdana,sans-serif">Research Scientist,</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">New York
University Abu Dhabi,</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Experimental Research Building</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Building C1, Saadiyat Island</span><br><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Abu Dhabi, UAE</span></div><div dir="ltr"><span style="font-family:verdana,sans-serif;color:rgb(51,51,255)">Phone no:
+971-561976358</span><p style="margin-bottom:0.0001pt">







</p><p><span style="font-family:serif,serif;color:rgb(51,51,255)"> <br></span></p></div></div></div></div></div></div>