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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi Tom<o:p></o:p></p><p class=MsoNormal>Thanks a lot. It showed that “No residues specific for swapping” when I work on my pdf, what should I do? By the way, the DNA is dsDNA, is there any way to replace the pair of DNA together?<o:p></o:p></p><p class=MsoNormal>Best regards<o:p></o:p></p><p class=MsoNormal>Gary<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b>From:</b> Tom Goddard <goddard@sonic.net> <br><b>Sent:</b> Monday, July 26, 2021 11:21 AM<br><b>To:</b> gren@lbl.gov<br><b>Cc:</b> Azad, Roksana via Chimera-users <chimera-users@cgl.ucsf.edu><br><b>Subject:</b> Changing DNA sequence<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Gary,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> The swapna command lets you change a nucleic acid base, for example, to change residue 18 in chain C from a T to a G use<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>open 1rsb<o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>swapna G :18.C<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Documentation for swapna<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span><a href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html">https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Tom<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Jul 26, 2021, at 1:31 AM, <<a href="mailto:gren@lbl.gov">gren@lbl.gov</a>> <<a href="mailto:gren@lbl.gov">gren@lbl.gov</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Dear Tom<o:p></o:p></p></div><div><p class=MsoNormal>Thanks for many answers to our previous questions.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>I have one more question to our loved Chimera program.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>I have a NDA model (PDB), but the sequence is not right. Is there any way to use this DNA model to generate a new model with a right order of sequence? In other word, if is there an automatic/ simple method (by comment lines) to replace the sequence by the correct one in Chimera?<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Thanks a lot!!<o:p></o:p></p></div><div><p class=MsoNormal>Gary<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Gang (Gary) Ren, PhD</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Lawrence Berkeley National Laboratory</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Molecular Foundry, Room: 2220</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>1 Cyclotron Road, MS 67R2206</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Berkeley CA 94720-8197</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Phone: (510) 495-2375; Fax: (510) 486-7268</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'>Email:<span class=apple-converted-space> </span><a href="mailto:gren@lbl.gov"><span style='color:#0563C1'>gren@lbl.gov</span></a>;<span class=apple-converted-space> </span></span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Ink Free"'><a href="https://rengroup.lbl.gov/"><span style='color:#0563C1'>https://rengroup.lbl.gov/</span></a></span></b><o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>