<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">For the purposes of sessions, molecules/atoms/bonds created by Chimera's "core" functionality can be treated differently than those created by Chimera tools (e.g. Volume Tracer), and named selections is an instance of such a difference. Basically, the core functionality that restores the named selections can only reference atoms/bonds also restored by the core functionality and can't reference the atoms/bonds being created by Volume Tracer during the session restore, so those atoms/bonds don't make it into the named selection.<div><br></div><div>This is a design issue and the programmers will talk about it and see what we can do to remedy it. But for now, you're kind of stuck unfortunately. I will open a bug report on this issue and include you on the cc list so that you can follow whatever progress we make on it.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Dec 8, 2008, at 1:02 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Giovanni,<br>I thought markers and atoms would be treated exactly the same, but now <br>testing with the marker file I also see this bug.<br><br>I see a problem even without using named selections: when I open the <br>marker file, select one marker, save the session, quit, and restart <br>the session, the marker is no longer selected.<br><br>We will look into this problem - thanks for reporting it!<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br>On Dec 8, 2008, at 11:09 AM, Giovanni Cardone wrote:<br><br><blockquote type="cite">Hi Elaine,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">sorry I did not give enough details. My problem is not with atoms in <br></blockquote><blockquote type="cite">a model, but with bonds and atoms in a marker set.<br></blockquote><blockquote type="cite">Here is an example: I open tripod.cmm (given below), I select just <br></blockquote><blockquote type="cite">one bond and one atom, name the selection as oneside, finally save <br></blockquote><blockquote type="cite">the session as test.py.<br></blockquote><blockquote type="cite">In the session file, I have the following line:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>savedSels = [('oneside', [])]<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">and if I reopen the session and recall the named selection, nothing <br></blockquote><blockquote type="cite">is selected.<br></blockquote><blockquote type="cite">Thank you,<br></blockquote><blockquote type="cite">Giovanni<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">tripod.cmm<br></blockquote><blockquote type="cite"><marker_set name="markers in a triangle"><br></blockquote><blockquote type="cite"><marker id="1" x="42.352" y="29.099" z="50.347" radius="0.5"/><br></blockquote><blockquote type="cite"><marker id="2" x="37.892" y="29.805" z="44.673" radius="0.5"/><br></blockquote><blockquote type="cite"><marker id="3" x="32.449" y="26.829" z="48.569" radius="0.5"/><br></blockquote><blockquote type="cite"><link id1="2" id2="1" r="1" g="1" b="1" radius="0.2"/><br></blockquote><blockquote type="cite"><link id1="3" id2="2" r="1" g="1" b="1" radius="0.2"/><br></blockquote><blockquote type="cite"><link id1="1" id2="3" r="1" g="1" b="1" radius="0.2"/><br></blockquote><blockquote type="cite"></marker_set><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Dec 8, 2008, at 1:50 PM, Elaine Meng wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Giovanni,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I can't tell what you did from what you said.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">The proper procedure is to first select those markers or atoms, <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">then name the selection. Then later you can use that name either <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">in the Select menu to make those markers or atoms selected again, <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">or in the command line, which would just perform the command on <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">those markers but not make them selected again.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">In my tests (Dec 7 build) this works fine. I don't have markers <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">handy, so here is an example with atoms. With markers you could <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">take a different approach to select them in the first place, but <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the remaining steps would be the same.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Example:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">open 1zik<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">select @ca<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> (or use Select menu to select some set of atoms,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> or Volume Tracer or interactive picking to select markers)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">namesel alphacarbs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> (or use Select... Name Selection to give that current selection a <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">name)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">[...now you could clear or change the selection...]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">rep sphere alphacarbs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> (or use Select... Named Selections... alphacarbs to regenerate <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the selection,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> then do something to it with the Actions menu)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I hope this helps,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Elaine<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-----<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">University of California, San Francisco<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Dec 8, 2008, at 10:32 AM, Giovanni Cardone wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi all,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I am trying to save a selection of a subset of markers as a named<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">selection. However, the named selection results empty: is it a <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">normal<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">behavior?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I am using Chimera version 1 build 2552.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks in advance,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Giovanni<br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>