<div dir="ltr">Summary after some investigation on my part:<div><br></div><div>The MTZ file in question was generated from a cryo-EM map using phenix.map_to_structure_factors. Due to the large box size of cryo-EM maps, such files tend to be <i>huge</i> - in this case, 1.8 billion reflections, about 800 times larger than the largest crystallographic dataset in the wwPDB. That alone wouldn't necessarily be a problem, but as well as the map amplitudes and phases (F/PHI), the MTZ output also contains a (undocumented, as far as I'm aware) "F-obs/SIGF-obs" array - the data type normally used to store crystallographic observations. Clipper interprets this as such, and tries to generate a set of live-recalculating maps. This is where things were going a bit awry: the extreme number of reflections broke some (naive) assumptions I'd made in the outlier rejection step, causing it to blow out from <1 second to almost 5 hours (!) - that's now been fixed (will be in the next full or dev release, whichever comes first), which should have the knock-on effect of making the loading of large crystallographic datasets much faster. On my Windows laptop (32 GB RAM, 32 GB swap) it manages to eventually generate the maps; on my Linux desktop (32 GB RAM, 2 GB swap) it eventually gets killed when it runs out of memory. The upshot right now:</div><div><br></div><div>- unless you have a very good reason to do otherwise, just work directly with the cryo-EM map rather than converting to structure factors first.</div><div>- if you do need to be working with structure factors, you can use the Reflection File Editor in the Phenix GUI to copy just the F/PHI column to a new MTZ. That opens in about 2-3 minutes and behaves as expected.</div><div><br></div><div>I'll also look into adding a GUI option to choose which columns to actually turn into maps when a multi-dataset MTZ file is opened.</div><div><br></div><div>-- Tristan</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jan 13, 2023 at 8:22 AM André Graça via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg1981043183576180725">
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<p class="MsoNormal">Hi everyone!<span lang="EN-GB"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">Is there any known issue with Clipper plugin for ChimeraX?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">After installing clipper and restarting ChimeraX, the software is not responding after I execute the Open command.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">I expect that it takes some time to open an .mtz file as the map needs to be calculated, however I have waited more than 45 minutes and ChimeraX keeps unresponsive…<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">I am using Chimera 1.5 and I installed the (hopefully compatible) version of Clipper 0.19.0<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">Did anyone faced the same problem? Let me know if you have a fix or trick ;)<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">Thanks for any feedback in advance,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB">André<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span><u></u> <u></u></span></p>
<p class="MsoNormal"><span>____________________<u></u><u></u></span></p>
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