<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Michael,<div class=""><br class=""></div><div class=""> I don't see the bug you mention. In Chimera 1.15 using 1a0s, the example I gave in the previous email, after I use meshmol I can still go back and for instance change under Unit Cell / Options to showing 2 1 1 unit cells, press Make Copies, and it all continues to work. Maybe the Molecule menu at the top of the Unit Cell panel somehow got set to the meshmol outline model which does not have any symmetry parameters associated with it.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 9, 2021, at 11:29 AM, Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="">michael.elbaum@weizmann.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="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; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi again,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">One bug-let. Once I invoke the meshmol, I can no longer go back to the Unit Cell tool to create a new lattice, even if I deselect or even delete the new model generated from the Outline. The lattice parameters have disappeared. Hard to say if this is worth fixing, but just to be aware...</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">best,<br class="">Michael<br class=""></div></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none; display: inline-block; width: 707.546875px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Chimera-users <<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" class="">chimera-users-bounces@cgl.ucsf.edu</a>> on behalf of Michael Elbaum<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, January 9, 2021 7:46:32 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Tom Goddard; Chimera<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] view along a crystal axis</font><div class=""> </div></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none;" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Elaine and Tom,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks for your suggestions. They were very helpful. A combination of the meshmol and align and the "old way" works well. There is still an arbitrary rotation in the visible plane. (Is there an align command that works along the x axis rather than the line of sight?) To take care of that I choose two "atoms" along an orthogonal axis, align those, and then if necessary 'turn y 90'. It's not automatic but seems to be precise.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">best wishes,</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Michael<br class=""></div></div><hr tabindex="-1" style="display: inline-block; width: 707.546875px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, January 9, 2021 2:06:03 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Chimera<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>Michael Elbaum<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] view along a crystal axis</font><div class=""> </div></div><div class="">Hi Michael,<div class=""><br class=""></div><div class=""> A small additional trick can let you align the view along an axis. You can turn the unit cell outline into a stick display made of fake atoms and bonds using the "meshmol" command. Then you can select two of the outline corner atoms and use the align command.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>open 1a0s</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span># Use menu Tools / Higher-Order Structure / Unit Cell to show copies and cell outline</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span># Ctrl-click on cell outline to select it</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>meshmol #0 1</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span># Select two corner "atoms" of the meshmol outline, ctrl click, then shift ctrl click.</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>align sel</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>set projection orthographic</div><div class=""><br class=""><div class=""><span id="cid:38EFE46A-46C7-4C59-8C75-8BD4719342A8"><1a0s_cell.jpg></span><br class=""><blockquote type="cite" class=""><div class="">On Jan 8, 2021, at 9:32 AM, 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 Michael,<br class="">I can't think of a direct way to align the view on a crystallographic axis... there is an "align" command to exactly align specified atoms along the line of sight in the center of the window:<br class=""><br class=""><<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/align.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/align.html</a>><br class=""><br class="">However, there may not be atoms that lie exactly along or parallel to the crystallographic axis, or it may not be easy to identify them. <br class=""><br class="">One roundabout way might be to use the Crystal Contacts tool (in menu under Tools... Higher-Order Structure) and click "Show Contacts" which shows the outline as markers and links. Markers are essentially fake atoms, so you could select the two corners of the outline box you want to align (Ctrl-click, Shift-Ctrl-click) and then use command "align sel" ... then hide or delete the markers and links after you get the desired alignment.<br class=""><br class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html</a>><br class=""><br class="">You might not want that in the center of the window, however, so additional translation ("move" commands) may be required afterwards.<br class=""><<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html</a>><br class=""><br class="">I couldn't do the "atom" selection with the box shown by Unit Cell because I think it is just a mesh and the whole box gets selected instead of corners.<br class=""><br class="">Other related commands...<br class=""><br class="">Command "reset" will give coordinate Z axis along the line of sight.<br class=""><br class="">Command "set projection orthographic" may be helpful to turn off perspective.<br class=""><br class="">Since the alignment is somewhat of a rigamarole, you may prefer to keep doing it your current way!<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><br class=""><br class=""><blockquote type="cite" class="">On Jan 8, 2021, at 6:09 AM, Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="">michael.elbaum@weizmann.ac.il</a>> wrote:<br class=""><br class="">Hi. I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this.<br class="">thanks for your help,<br class="">Michael<br class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription:<span class="Apple-converted-space"> </span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription:<span class="Apple-converted-space"> </span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></span></div></blockquote></div><br class=""></div></body></html>