<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I should clarify that I implemented it in the dialog that the “select chain(s)…” button in the model panel shows. That was easy. I <i class="">didn’t</i> implement it in the main Select->Chain menu, since the code modifications would be considerably more complicated. The latter is still worth doing but won’t happen immediately.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 13, 2016, at 10:21 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Jochen,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Since it was pretty easy I went ahead and implemented your suggestion. It will be in the next daily build and release candidate.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div></div><div class=""><blockquote type="cite" class=""><div class="">On Jun 13, 2016, at 1:30 AM, Jochen Baßler <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de" class="">jochen.bassler@bzh.uni-heidelberg.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class=""><div class=""><div class=""><div class="">Hi Eric,</div><div class=""><br class=""></div><div class="">Yes, the new release candidate is having all the important information in the reply log file and it is shown below as Elaine indicated.</div><div class="">Thank you for this new feature. Maybe one could extend this a bit further?</div><div class="">Since these informations are already imported, one could implement them into the "select Chain" menu, which one can access via the model panel?</div><div class="">Then it would be very easy to click or select a protein of interest.</div><div class=""><br class=""></div><div class="">Thanks for the feedback and the information. (The only bad point is that this new version is not running on my mac wit OSX 10.7, So I have to update also here…)</div><div class=""><br class=""></div><div class="">Best wishes</div><div class=""><br class=""></div><div class="">Jochen</div><div class=""><br class=""></div></div></div><div class=""><br class=""></div><div class=""><br class=""></div><span id="OLK_SRC_BODY_SECTION" class=""><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);" class=""><span style="font-weight:bold" class="">From: </span> Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><span style="font-weight:bold" class="">Reply-To: </span> Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><span style="font-weight:bold" class="">Date: </span> Friday, 10June, 2016 6:54 PM<br class=""><span style="font-weight:bold" class="">To: </span> J B <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de" class="">jochen.bassler@bzh.uni-heidelberg.de</a>><br class=""><span style="font-weight:bold" class="">Cc: </span> Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><span style="font-weight:bold" class="">Subject: </span> Re: [Chimera-users] Splitting an pdb with multiple proteins<br class=""></div><div class=""><br class=""></div><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">Hi Jochen,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Support for chain descriptions coming from mmCIF files (rather than PDB files) was only added after the 1.10.2 release. Please try the current 1.11 release candidate and see how that works.</div><div class=""><br class=""></div><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""><div class=""><div class="">On Jun 10, 2016, at 1:36 AM, Jochen Baßler wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class=""><div class=""><div class=""><div class="">Dear Elaine, Eric,</div><div class=""><br class=""></div><div class="">Thanks a lot for your fast replay.</div><div class="">I imported 3jct and 5hau to test your suggestions, but the reply log just contained :</div><div class=""><br class=""></div><div class=""><div class="">[MMLIB:WARNING] monomer description not found in zipfile for '4SU'</div><div class="">[MMLIB:WARNING] monomer description not found in zipfile for '5MC'</div></div><div class=""><br class=""></div><div class="">How can I activate the status message?</div><div class="">With the mouse I can see the chain number near the mouse pointer, but there is no information below at the main window.</div><div class=""><br class=""></div><div class="">(I am running chimera version 1.10.2)</div><div class=""><br class=""></div><div class="">Best wishes</div><div class=""><br class=""></div><div class="">Jochen</div><div class=""><div class=""><br class=""></div></div></div></div><div class=""><br class=""></div><span id="OLK_SRC_BODY_SECTION" class=""><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);" class=""><span style="font-weight:bold" class="">From: </span> Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><span style="font-weight:bold" class="">Date: </span> Friday, 10June, 2016 1:51 AM<br class=""><span style="font-weight:bold" class="">To: </span> "<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><span style="font-weight:bold" class="">Cc: </span> J B <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de" class="">jochen.bassler@bzh.uni-heidelberg.de</a>><br class=""><span style="font-weight:bold" class="">Subject: </span> Re: [Chimera-users] Splitting an pdb with multiple proteins<br class=""></div><div class=""><br class=""></div><div class=""><meta http-equiv="Content-Type" content="text/html charset=windows-1252" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">It is also listed in the reply log as the structure is opened.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div></div><br class=""><div style="" class=""><blockquote type="cite" class=""><div class="">On Jun 9, 2016, at 4:49 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Jochen,<br class="">This information is already imported, and when you mouse over the chain, it is shown in the “status message” area across the bottom of the Chimera window. <br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html</a>><br class=""><br class="">I tested just now, and the information is retained and can be shown in the same way after “split” is used. However, it is not automatically used as the model names.<br class="">I hope this helps,<br class="">Elaine<br class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Jun 9, 2016, at 4:05 AM, Jochen Baßler <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de" class="">jochen.bassler@bzh.uni-heidelberg.de</a>> wrote:<br class=""><br class="">Hi,<br class=""><br class="">I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT).<br class="">Is there a way to import the information from the pdb database, which tells you the name of the chains?<br class="">Chain A = rpl2<br class="">Chain B = Rpl4 etc.<br class="">Cool would be to split the pdb into multiple models that have the name from the pdb database.<br class="">(It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure)<br class=""><br class="">Thanks for suggestions and solutions<br class=""><br class="">Best wishes<br class=""><br class="">Jochen<br class=""><br class=""></blockquote><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></div></span></div></blockquote></div><br class=""></div></div></div></span></div>
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