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 <[email protected]<mailto:[email protected]>> 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<https://aka.ms/o0ukef> ________________________________ From: CCP4 bulletin board <[email protected]<mailto:[email protected]>> on behalf of Gloria Borgstahl <[email protected]<mailto:[email protected]>> Sent: Tuesday, November 26, 2024 11:50:18 PM To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> 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]<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!Bq9Q2A7BeRUUD1gN0rjsxbHV922Cq9669_rUfVpiegzWw9tBE93cCZTbltQNxbYsugO_sU-a_0EoSrAUHaJgXNH7jaJ1jVE$> ________________________________ 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. 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 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/
