Alejandro, It sounds like the map is over weighted in refinement, causing distortion of the stereochemistry. Lower your RMSD target or Map Weighting to improve the stereo chemistry in the model. At 3.7 Å a bond RMSD of 0.005 Å or less is reasonable.
Best regards, Mark Mark Andrew White, Ph.D. Professor of Biochemistry & Molecular Biology, Director, SCSB Macromolecular X-ray Laboratory UTMB, Galveston, TX 409.747.4747 https://xray.utmb.edu<https://xray.utmb.edu/> ________________________________ From: Mailing list for users of COOT Crystallographic Software <[email protected]> on behalf of Alejandro Buschiazzo <[email protected]> Sent: Thursday, June 5, 2025 7:30 AM To: [email protected] <[email protected]> Subject: Python script to process a large list of residues for restrained geometry idealization External Email Warning: Do not click links or open attachments unless you recognize the sender and expect the content. UTMB Email Phishing Awareness<https://www.utmb.edu/infosec/resources/externalemail> Dear cooters Could anyone help me out in efficiently addressing the following problem? I have a long list of residue side chains, whose planarity is to be corrected. I am at the end of refinement (against a 3.7Å res cryoEM map), so already happy with many other validation indices (and especially, map to model cross correlation), so would want to change the model as little as possible. My model is huge (many chains), which explains the long list of outliers. Can I feed this properly into Coot 1.1.15, such that self restrains are calculated (let’s say using a 5Å sphere for the whole molecule; and that a pretty tight Gemann-McClure alpha parameter is set, like 0.01-0.03), and that then each of the listed residues gets ‘geometry-idealized’? Given the many NCS relatives (many chains are identical in my complex), doing this by hand is extremely slow, each time I say yes to a correction, there’s a super long calculation (NCS matrix refinement) going through ALL chains ….making this simple approach impracticable. Many thanks in advance! Alejandro -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 ext. 120 Fax: +598 25224185 https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/ ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
