Hi Harry First off I would look at quality metrics. For the structures from the same paper you will need to check what the differences are in the paper and choose what’s closest to what you have need (experimental conditions etc) assuming they all have similar quality
As a secondary priority you will want to look at number of restraints (and especially in the region of interest) Note I would expect the more modern structures from cyana and aria to better due to improved methodologies Regards Gary -------------------------------------------------------------------- Dr Gary S Thompson NMR Facility Manager CCPN CoI & Working Group Member Wellcome Trust Biomolecular NMR Facility School of Biosciences, Faculty of Natural Sciences University of Kent, Canterbury, Kent, England, CT2 7NZ tel: 01227 82 7117 e-mail: g.s.thomp...@kent.ac.uk<mailto:g.s.thomp...@kent.ac.uk> orchid: orcid.org/0000-0001-9399-7636<https://urldefense.com/v3/__http:/orcid.org/0000-0001-9399-7636__;!!JFdNOqOXpB6UZW0!5pL_seJsFx0GRaDgwaLL0h3tmVktbehHKv07ZEZEcqZMKbC_s464UgFam-zmCFabTW0x$> -------------------------------------------------------------------- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Harry Powell <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> Date: Wednesday, 3 May 2023 at 11:45 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] choosing an NMR structure from PDB CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Hi folks I was wondering. If there is a UniProt entry (for example, P01132, but there are plenty of others) for which I want the “best” (whatever that might mean) representative _experimental_ structure (i.e. not one of these new-fangled predicted models that some folk say have removed the need for actually doing experiments), but there are only NMR models - how do I choose? I don’t mean “which model from the ensemble do I choose” - that’s a different question. For P01132, for example, I could choose (from the PDB) 1A3P, 1EGF, 1EPG, 1EPH, 1EPI, 1EPJ, 1GK5 or 3EGF. Note that some of these are from the same paper, so may be in different conditions (e.g. pH). All except the first (1A3P) cover the same bit of sequence. Specifically, what should I look for in the downloadable files (mmCIF, for example) from the PDB? Thoughts? Harry ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7CG.S.Thompson%40kent.ac.uk%7Cdae9af07a7934523289d08db4bc380d4%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638187075277708989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VXUCSdQR%2B%2BlHvD%2FDZQi%2FBcRBNIEkiMziOtboUXSUT08%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C01%7CG.S.Thompson%40kent.ac.uk%7Cdae9af07a7934523289d08db4bc380d4%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638187075277708989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=kg3UcX0VdLg3Mpa0gxDMu5W9YMv%2BjE9cLjUHr2twY%2Bg%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C01%7CG.S.Thompson%40kent.ac.uk%7Cdae9af07a7934523289d08db4bc380d4%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638187075277708989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UimgK9Z%2BvOlaKxnF%2B4BanvF1eerK6yMl9nIxPIn3Rmc%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C01%7CG.S.Thompson%40kent.ac.uk%7Cdae9af07a7934523289d08db4bc380d4%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638187075277708989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4rWORcxteFdPePlmM%2BZyJ1amJbpFbYG3%2FHmJ0cwB6ek%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ######################################################################## 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/
