Yes, I agree this is a good point. We had an example at a CCP-EM workshop where the participant’s map turned out to have the wrong hand. I’m embarrassed to say that it took Tristan Croll (sitting next to me) to notice that the helices were left-handed! Anyway, flipping the hand was quick and easy in ChimeraX, and the correct hand unambiguously gave the right answer. Since emplace_local only takes typically 20s to 2 minutes to run, it doesn’t take a long time to check the other hand if you don’t get a clear answer with the first hand. Probably we should put in an option to test the other hand automatically if there isn’t a clear answer (LLG > 60, say) for the original hand.
Randy > On 28 Nov 2024, at 09:31, Guillaume Gaullier <guillaume.gaull...@kemi.uu.se> > wrote: > > Hello Matthew, > > This is a very good point. With good maps one can tell if it’s the correct > hand by visually inspecting the alpha-helices (or from features of the > quaternary structure for some complexes), but sometimes it is more difficult. > I don’t know how em_placement and emplace_local behave with left-handed maps. > My guess is that they would give a solution but with a very poor LLG score. > > I have accidentally run ModelAngelo [1, 2] on a left-handed map and in this > case the failure mode is very clear: you get many disconnected short > fragments in a left-handed map, but a much more complete and connected atomic > model in a right-handed map. But the run time is in the same order of > magnitude (a bit worse when using the left-handed map). > > If em_placement and emplace_local fail faster on left-handed maps, that would > be interesting to know (maybe I’ll test that sometime). But I don’t think > there’s a hand detection method faster than visual inspection, and if the > resolution is too poor for that, then systematically running rigid-body > fitting and automated model building against both hands seems warranted. > > Cheers, > > Guillaume > > [1]: https://github.com/3dem/model-angelo > > [2]: https://doi.org/10.1038/s41586-024-07215-4 > > >> On 27 Nov 2024, at 20:29, Matthew Snee <matthew.sne...@manchester.ac.uk> >> wrote: >> >> Hi Gloria >> >> I didn’t see this mentioned (perhaps I missed it). But if you are struggling >> to get your initial docking solution, do check that your hand is correct. >> If your map is good enough you can possibly get it by building small trial >> sections (alpha helices can be good), for more challenging lower resolution >> ones you can just try both. >> >> Best wishes >> >> Matthew. >> >> Sent from Outlook for iOS >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Gloria >> Borgstahl <gborgst...@gmail.com> >> Sent: Tuesday, November 26, 2024 11:50:18 PM >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> Subject: [ccp4bb] cryoEM molecular replacement This Message Is From a New >> External Sender You have not previously corresponded with this sender. >> Please exercise caution when opening links or attachments included in this >> message. >> Hello Friends, >> We are finally using cryoEM when the crystallography got too hard! We have >> a crystal structure for the hexamer. What is the easiest software tool to >> swing a monomer or hexamer into the cryoEM density? >> Thank you, Gloria >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> [jiscmail.ac.uk] >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen >> avsändaren och vet att innehållet är säkert. >> CAUTION: Do not click on links or open attachments unless you recognise the >> sender and know the content is safe. > > Page Title > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
