The clash score is also impressively high. Your map may have the incorrect hand. Have you tried flipping it?
Best wishes Reza ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Martyn Winn - STFC UKRI <00007c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> Sent: 10 January 2024 4:51 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [EXTERNAL] Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map. You can also try the CCPEM list for more cryoEM-orientated advice https://www.jiscmail.ac.uk/CCPEM<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_CCPEM&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=2OrQybU3Ol8yXPT5Pr4ePy2APoCdK9s7hy3XcBfDxB4&e=> and look in CCP-EM for more fitting, refinement, validation tools. Certainly, the map doesn’t look 3A, unless you have filtered it for these pictures. The CC for the middle and C-terminal domains is not just low, but essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So I think you need to look again at the initial fitting. HTH Martyn From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Basil Greber Sent: 10 January 2024 08:12 To: ccp4bb <ccp4bb@jiscmail.ac.uk> Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map. Are you confident that your 3 Å resolution is correct? The map in the picture you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is apparently 20 Å (?). Basil Gesendet mit der mobilen Mail App Am 10.01.24 um 05:57 schrieb Ketul Saharan Von: "Ketul Saharan" <ktsaharan1...@gmail.com> Datum: 10. Januar 2024 An: CCP4BB@JISCMAIL.AC.UK Cc: Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map. Dear CCP4 community, I am building a structure model from ~3.0 Å resolution cryo-EM map. The structure consists of seven chains, with each chain containing an N-, middle, and C-terminal domain. Although I attempted to directly fit the Alfa-fold model, it became evident that the protein exhibited some movement, leading to poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold model into two parts: i) the N-terminal and ii) the middle and C-terminal domain. These fragments were then fitted into the map. After a few rounds of refinement using coot and phenix, the model effectively fitted all seven chains. The refinement resulted in a model to map correlation (CC mask) of over 60% for the N-terminus. However, even though the model appeared to fit well inside the map, particularly in the middle and C-terminus regions, the refining consistently resulted in a map to model correlation of 0%. For your perusal, I have included the snapshot of the phenix refinement results, the correlation graph, and the fitted model within the map (displaying one chain out of seven). I am not able to figure out why the correlation is so poor even after fine fitting of model to map. Any support in resolving this issue would be much appreciated. Thank, Ketul Saharan -- Ketul Saharan Senior Research Fellow (Ph.D. Scholar) Laboratory of Macromolecular Crystallography (Lab-8) Institute of Life Sciences Nalco Square, Chandrasekharpur Bhubaneswar – 751023 Odisha State, INDIA Phone: +91 8708290889 [https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 124.png<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1qYE-5Fge1M99zbkUt-5Fg4JF3bNfEyDUelkS_view-3Fusp-3Ddrive-5Fweb&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=Mjs-SQCTUY825jEQWMt5kyRM4gP3VCZYCIIcquH5aus&e=>[Image removed by sender.] [https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] correlation.tif<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1bogOk15bImYXSLCPcnrUfC9gRH0cGame_view-3Fusp-3Ddrive-5Fweb&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=cVtL8i32mlgU6UWPBzpKBN0tDXjLH6LMWEk4cfCkoEw&e=>[Image removed by sender.] [https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] map to model.tif<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1y-2DQXMOwWslOTg2PRjS91PFf-2Dgh1obiEt_view-3Fusp-3Ddrive-5Fweb&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=gg9hzqFIZuZnJPmptl85bCVhapcj6bLwhmN1CdWV14w&e=>[Image removed by sender.] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=t7WW1ZsJoI0gibfxz42GpLQz8SpTY9ZZ8TJ3W2rtOt8&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=t7WW1ZsJoI0gibfxz42GpLQz8SpTY9ZZ8TJ3W2rtOt8&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=wrSHAkh1Qubqd-dNnifT_cfYiS6hsyu7yM8hs1qRKiDhno82lReW1XUDhNOgIq1S&s=t7WW1ZsJoI0gibfxz42GpLQz8SpTY9ZZ8TJ3W2rtOt8&e=> ######################################################################## 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/
