<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><div><div>Hi Eric,</div><div><br></div><div>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>Thank you for this new feature. Maybe one could extend this a bit further?</div><div>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>Then it would be very easy to click or select a protein of interest.</div><div><br></div><div>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><br></div><div>Best wishes</div><div><br></div><div>Jochen</div><div><br></div></div></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br><span style="font-weight:bold">Reply-To: </span> Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 10June, 2016 6:54 PM<br><span style="font-weight:bold">To: </span> J B <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de">jochen.bassler@bzh.uni-heidelberg.de</a>><br><span style="font-weight:bold">Cc: </span> Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: [Chimera-users] Splitting an pdb with multiple proteins<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jochen,<div><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><br></div><div>--Eric</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div><br><div><div>On Jun 10, 2016, at 1:36 AM, Jochen Baßler wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><div><div>Dear Elaine, Eric,</div><div><br></div><div>Thanks a lot for your fast replay.</div><div>I imported 3jct and 5hau to test your suggestions, but the reply log just contained :</div><div><br></div><div><div>[MMLIB:WARNING] monomer description not found in zipfile for '4SU'</div><div>[MMLIB:WARNING] monomer description not found in zipfile for '5MC'</div></div><div><br></div><div>How can I activate the status message?</div><div>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><br></div><div>(I am running chimera version 1.10.2)</div><div><br></div><div>Best wishes</div><div><br></div><div>Jochen</div><div><div><br></div></div></div></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 10June, 2016 1:51 AM<br><span style="font-weight:bold">To: </span> "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br><span style="font-weight:bold">Cc: </span> J B <<a href="mailto:jochen.bassler@bzh.uni-heidelberg.de">jochen.bassler@bzh.uni-heidelberg.de</a>><br><span style="font-weight:bold">Subject: </span> Re: [Chimera-users] Splitting an pdb with multiple proteins<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><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="color: rgb(0, 0, 0); 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=""><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></div></div></div></span></body></html>