Hi Tom,<br>Very nice example. Really big help! Just updated to the newest Chimera version, done!<br>Thanks again for your time and patience.<br><br>Chen<br><br><br>&gt;&nbsp;-----Original&nbsp;Messages-----<br>&gt;&nbsp;From:&nbsp;"Tom&nbsp;Goddard"&nbsp;&lt;goddard@sonic.net&gt;<br>&gt;&nbsp;Sent&nbsp;Time:&nbsp;Wednesday,&nbsp;April&nbsp;13,&nbsp;2016<br>&gt;&nbsp;To:&nbsp;"Cheng-Chen&nbsp;Xu"&nbsp;&lt;xucc@wh.iov.cn&gt;<br>&gt;&nbsp;Cc:&nbsp;<br>&gt;&nbsp;Subject:&nbsp;Re:&nbsp;[Chimera-users]&nbsp;fivefold&nbsp;rotate&nbsp;command<br>&gt;&nbsp;<br>&gt;&nbsp;Hi&nbsp;Chen,<br>&gt;&nbsp;<br>&gt;&nbsp;&nbsp;&nbsp;Yes&nbsp;you&nbsp;can&nbsp;rotate&nbsp;the&nbsp;pentamers&nbsp;of&nbsp;a&nbsp;T=1&nbsp;icosahedral&nbsp;capsid&nbsp;in&nbsp;Chimera&nbsp;using&nbsp;the&nbsp;“turn”&nbsp;and&nbsp;“sym”&nbsp;commands.&nbsp;&nbsp;The&nbsp;hardest&nbsp;part&nbsp;is&nbsp;figuring&nbsp;out&nbsp;the&nbsp;direction&nbsp;of&nbsp;the&nbsp;5-fold&nbsp;axis.&nbsp;&nbsp;Here’s&nbsp;an&nbsp;example<br>&gt;&nbsp;<br>&gt;&nbsp;        open&nbsp;2bpa<br>&gt;&nbsp;        open&nbsp;2bpa<br>&gt;&nbsp;        sym&nbsp;#1&nbsp;update&nbsp;true&nbsp;coord&nbsp;#0<br>&gt;&nbsp;        #&nbsp;Select&nbsp;opposite&nbsp;pentamers&nbsp;by&nbsp;hand&nbsp;(10&nbsp;monomers&nbsp;total)&nbsp;with&nbsp;mouse&nbsp;and&nbsp;up-arrow&nbsp;key<br>&gt;&nbsp;        define&nbsp;axis&nbsp;sel<br>&gt;&nbsp;        turn&nbsp;a1&nbsp;5&nbsp;model&nbsp;#1<br>&gt;&nbsp;<br>&gt;&nbsp;I&nbsp;open&nbsp;2&nbsp;copies&nbsp;of&nbsp;the&nbsp;virus,&nbsp;the&nbsp;first&nbsp;copy&nbsp;(#0)&nbsp;just&nbsp;serves&nbsp;as&nbsp;a&nbsp;reference&nbsp;coordinate&nbsp;system&nbsp;when&nbsp;I&nbsp;move&nbsp;the&nbsp;second&nbsp;copy&nbsp;(#1).&nbsp;&nbsp;The&nbsp;sym&nbsp;command&nbsp;makes&nbsp;the&nbsp;60&nbsp;copies&nbsp;of&nbsp;#1&nbsp;for&nbsp;the&nbsp;full&nbsp;virus&nbsp;and&nbsp;the&nbsp;“update”&nbsp;option&nbsp;says&nbsp;to&nbsp;update&nbsp;all&nbsp;the&nbsp;positions&nbsp;when&nbsp;copy&nbsp;#1&nbsp;moves&nbsp;relative&nbsp;to&nbsp;#0.&nbsp;&nbsp;Then&nbsp;I&nbsp;define&nbsp;an&nbsp;axis&nbsp;(called&nbsp;a1)&nbsp;by&nbsp;selecting&nbsp;two&nbsp;opposite&nbsp;pentamers&nbsp;including&nbsp;the&nbsp;#1&nbsp;monomer.&nbsp;&nbsp;Then&nbsp;I&nbsp;rotate&nbsp;monomer&nbsp;#1&nbsp;about&nbsp;that&nbsp;axis&nbsp;by&nbsp;5&nbsp;degrees,&nbsp;and&nbsp;all&nbsp;the&nbsp;other&nbsp;60&nbsp;copies&nbsp;will&nbsp;move&nbsp;automatically&nbsp;to&nbsp;maintain&nbsp;symmetry.&nbsp;&nbsp;Here’s&nbsp;a&nbsp;movie&nbsp;illustrating&nbsp;the&nbsp;motion.<br>&gt;&nbsp;<br>&gt;&nbsp;        http://www.cgl.ucsf.edu/home/goddard/temp/spin_5fold.mp4<br>&gt;&nbsp;<br>&gt;&nbsp;&nbsp;&nbsp;Tom<br>&gt;&nbsp;<br>&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;On&nbsp;Apr&nbsp;11,&nbsp;2016,&nbsp;at&nbsp;8:42&nbsp;PM,&nbsp;Cheng-Chen&nbsp;Xu&nbsp;wrote:<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;Hi&nbsp;Chimera,<br>&gt;&nbsp;&gt;&nbsp;Is&nbsp;there&nbsp;anyway&nbsp;to&nbsp;rotate&nbsp;each&nbsp;pentamer&nbsp;around&nbsp;its&nbsp;own&nbsp;fivefold&nbsp;axis&nbsp;separately&nbsp;and&nbsp;simultaneously&nbsp;when&nbsp;dealing&nbsp;with&nbsp;a&nbsp;T=1&nbsp;icosahedral&nbsp;virus&nbsp;capsid?<br>&gt;&nbsp;&gt;&nbsp;Many&nbsp;thanks,<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;Chen<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;<br>&gt;&nbsp;&gt;&nbsp;_______________________________________________<br>&gt;&nbsp;&gt;&nbsp;Chimera-users&nbsp;mailing&nbsp;list:&nbsp;Chimera-users@cgl.ucsf.edu<br>&gt;&nbsp;&gt;&nbsp;Manage&nbsp;subscription:&nbsp;http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br>&gt;&nbsp;<br><br><br><br>