<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Yu,<div class=""><br class=""></div><div class="">Since I don’t know what S2 and S3 richer state is… I don’t know if this is going to help. </div><div class="">but, you can open, select and save pdb chains in chimera command line and view only the selected subunits:</div><div class=""><br class=""></div><div class="">Example:</div><div class="">1) View only the selected chain</div><div class="">~display</div><div class="">~ribbon</div><div class="">disp :.A-B</div><div class=""><br class=""></div><div class="">2) saving only selected PDB files </div><div class="">open 6DHO </div><div class="">select :.A-B</div><div class="">write selected 0 test.pdb </div><div class=""><br class=""></div><div class="">then follow step 1.</div><div class=""><br class=""></div><div class=""><div class="">if you don’t like cif file formats you can convert them in Phenix package (PDB tools).</div></div><div class=""><br class=""></div><div class="">Hope this helps,</div><div class="">David </div><div class=""><br class=""></div><div class=""><div class=""><div><blockquote type="cite" class=""><div class="">On Nov 24, 2018, at 11:28 AM, Yu Guo <<a href="mailto:yg2@kth.se" class="">yg2@kth.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Dear Sir/Madam,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""> I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much!<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Best wishes<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><span id="cid:E3FF4CF3-6629-43AF-BF94-99D694F0D770@ucsfguest.ucsf.edu"><6dho.cif></span><span style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""></div></blockquote></div><br class=""></div></div></body></html>