<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="">Hi Joe,<div class=""><br class=""></div><div class=""> These maps have both C6 and helical symmetry, and as I said before you should fit one copy of each of the two proteins and then apply symmetry with the sym command, for example,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sym #1 group c6 coord #0</div><div class=""><br class=""></div><div class="">where #1 is an atomic model and #0 is the map would apply C6 symmetry and the sym documentation shows how to also handle the helical part.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</a></div><div class=""><br class=""></div><div class=""> The method of randomly placing and optimizing fits and detecting collisions is simply not going to work for too many reasons to mention, and is the wrong approach anyways since you don’t want to create an assembly that does not follow the exact symmetry.</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><blockquote type="cite" class=""><div class="">On May 10, 2017, at 1:46 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</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; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Tom,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Apologies, I must have switched the numbers as I typed. The EM density is <span class="">EMD-6271 and <span class="">EMD-6270. If you fetch 6270 with fitted PDB's, it should be fairly obvious what I mean when it comes to fitting 2 different rings of proteins, however I wish to do this with my own structures in to their map, rather than the structures they have.</span></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""><span class=""><br class=""></span></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">The structures I have a simulations/homology models, so they don't contain any BIOMT/symmetry information, thus I think I'm left with the only option being fitting each protein individually. Since I plan to do this quite a lot, I'd rather not have to resort to doing it by hand (and if it can be scripted - all the better).</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I envisage the problem like this (correct me if you think this approach won't work though):</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">1. Open the first protein. Fit the first protein for each ring (1 monomer)</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">2. Continue to open models consecutively (or copy the existing one)</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">3. With each new model that is opened, fit it, but somehow determine if the same space is occupied with another model, if so, try elsewhere</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I believe the fit-in-map function can be given a random starting position, such that fitting in to different densities could be achieved without manual initial placement. I think the conceptual step I'm stuck on would just be knowing whether chimera has any means of knowing whether 2 PDBs are occupying the same space (and/or EM density) - and then effectively using this as a conditional to re-attempt placement?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks for the help thus far,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Joe</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">Joe Healey<br style="font-size: 10pt;" class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="text-decoration: underline;" class=""> </span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-size: 10pt;" class="">M.Sc. B.Sc. (Hons) MSRB</span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-size: 10pt;" class=""></span><div class=""><span style="font-size: 10pt;" class="">PhD Student</span></div><div class=""><span style="font-size: 10pt;" class="">MOAC CDT, Senate House</span></div><div class=""><span style="font-size: 10pt;" class="">University of Warwick<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Coventry<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">CV47AL<br class="">Mob: +44 (0) 7536 042620 | </span><span style="font-size: 10pt;" class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a></span></div><div class=""><span style="font-size: 10pt;" class=""><br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Jointly working in:<br class=""></span></div><div class=""><span style="font-size: 10pt;" class=""><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP" class="">Waterfield Lab</a><span class="Apple-converted-space"> </span>(<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">WMS </span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">Microbiology and Infecti</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">on Un</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">it)</span></span></div><div class=""><span style="font-size: 10pt;" class="">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP" class="">Gibson Lab</a> (Warwick Chemistry)<br class=""></span></div><div class=""><span style="font-size: 10pt;" class=""><br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Twitter:<span class="Apple-converted-space"> </span><a href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a> | </span><span style="font-size: 10pt;" class="">Website:<span class="Apple-converted-space"> </span></span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" style="font-size: 10pt;" class="">MOAC Page</a> | ORCID: <span class=""><a href="http://orcid.org/0000-0002-9569-6738" class="">orcid.org/0000-0002-9569-6738</a></span></div></div></div></div></div><hr tabindex="-1" style="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; display: inline-block; width: 867.296875px;" class=""><span style="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; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="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;" 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>10 May 2017 02:00:57<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Healey, Joe<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Multiple fitting of structures in to EM densities</font><div class=""> </div></div><div style="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;" class="">Hi Joe,<div class=""><br class=""></div><div class=""> It doesn’t look like EMDB 6720, mammalian respiratory supercomplex is made up of hexamer rings. Is that the structure you mean?</div><div class=""><br class=""></div><div class=""> In you have 3 or 4 stacked hexamer rings for each of 2 proteins and they are exactly symmetric, or at least the map was reconstructed by imposing symmetry, then I would only fit one copy of an atomic model, and then create all the other copies using the Chimera “sym” command so they are exactly placed according to the symmetry. If there really is no exact symmetry then you do have to fit each copy individually. The Chimera "Fit in Map” tool or equivalent fitmap command does a local optimization based on an initial placement of the atomic model in the map — it uses gradient ascent to maximize correlation — so it will just find a local best fit. So in this case I would hand place each copy of the atomic model, trying to get the position right to better than half the protein diameter (say 10 or 20 Angstroms) and the orientation angle not too far off (say no further than 60 degrees), then use the Chimera fitmap command or dialog on each. If the map is high resloution like EMDB 6720 at 3.6 Angstroms you can probably fit copies without them moving to an adjacent position. At much lower resolution like 15 Angstroms, the copies will tend to move all to the highest density. Then you need to use the fitmap sequence or symmetry options to take into account clashes between the copies.</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 class=""><blockquote type="cite" class=""><div class="">On May 9, 2017, at 8:07 AM, Healey, Joe wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" class="" 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; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Dear chimera team,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I have a large EM density I would like to fully populate with a number of copies of a protein. To be more specific, the EM density is of 2 concentric protein rings (EMDB-6720), and each concentric ring is stacked 3 or 4 times. Each ring is a hexamer, so I would like to populate every single ring with 6 copies of each protein (but the inner and outer rings are 2 different proteins).</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">What would be the best mechanism to iteratively import a protein, populate an EM density space, then move on to the next one? Currently, I think if I was to simply open several copies of the protein, they would probably all try to fit within the same EM density position, leaving the rest of the structure empty?</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">My apologies if this isn't totally clear, I've tried to explain it as best as I think I can. I'm happy to accept solutions in 'chimera language', python (or I also have Jaime's Pychimera installed).</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Many thanks</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" class="" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;"><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">Joe Healey<br class="" style="font-size: 10pt;"></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><br class=""></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="text-decoration: underline;"> </span><br class=""></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="font-size: 10pt;">M.Sc. B.Sc. (Hons) MSRB</span><br class=""></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="font-size: 10pt;"></span><div class=""><span class="" style="font-size: 10pt;">PhD Student</span></div><div class=""><span class="" style="font-size: 10pt;">MOAC CDT, Senate House</span></div><div class=""><span class="" style="font-size: 10pt;">University of Warwick<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">Coventry<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">CV47AL<br class=""><br class=""></span><span class="" style="font-size: 10pt;"></span></div><div class=""><span class="" style="font-size: 10pt;"><br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">Jointly working in:<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP" class="">Waterfield Lab</a><span class="Apple-converted-space"> </span>(<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; 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