THere must be some error in the calculation of the CC - or you are over optimistic about what constitutes a fit! What does the COOT density fit show? Eleanor
On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI < [email protected]> wrote: > You can also try the CCPEM list for more cryoEM-orientated advice > https://www.jiscmail.ac.uk/CCPEM 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 <[email protected]> *On Behalf Of *Basil > Greber > *Sent:* 10 January 2024 08:12 > *To:* ccp4bb <[email protected]> > *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" <[email protected]> > Datum: 10. Januar 2024 > An: [email protected] > 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 > > * 124.png > <https://drive.google.com/file/d/1qYE_ge1M99zbkUt_g4JF3bNfEyDUelkS/view?usp=drive_web>[image: > Image removed by sender.] * > > * correlation.tif > <https://drive.google.com/file/d/1bogOk15bImYXSLCPcnrUfC9gRH0cGame/view?usp=drive_web>[image: > Image removed by sender.] * > > * map to model.tif > <https://drive.google.com/file/d/1y-QXMOwWslOTg2PRjS91PFf-gh1obiEt/view?usp=drive_web>[image: > 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 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
