Hello, It’s also amazing how one can mess up bond lengths so badly without actually damaging the angles—very interesting!
In this instance, it looks like an amyloid fibril, so each peptide is likely nearly perfectly in one plane. This means that any problem would leave the dihedral angles fine (consistent with the perfect Ramachandran distribution shown). If the model were a bit stretched in all directions, most bonds would be too long but very few of the bond angles would be distorted (also consistent with the low number of bond angle outliers shown). Then, one reason why the model would be stretched in all directions could be that the pixel size of the cryoEM map is inaccurate (a bit larger than expected). It seems like you have already identified the problem with the amide cap, but it might be a good idea to check the pixel size calibration just in case. I hope this helps, Guillaume On 20 Feb 2025, at 02:50, Das, Abhinaba <[email protected]<mailto:[email protected]>> wrote: Hi Kasper, Yes, you are correct. There are 80 chains with 480 residues. Each of these 80 chains has a C-amide capping. It’s hexapeptide whose sequence we know and matches the density. Unlikely they need to be merged. More precisely, the number of NH2 present equals to number of bonds of unrealistic length. Somehow the program thinks that the ideal value for the terminal C-N linkage should be 2.329A but it’s an amide bond. Best, Abhi From: Kaspar Hollenstein <[email protected]<mailto:[email protected]>> Date: Wednesday, February 19, 2025 at 7:47 PM To: Das, Abhinaba <[email protected]<mailto:[email protected]>> Cc: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Low atom inclusion score error while depositing to PDB You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Abhinaba, Based on your screenshot of the validation summary, your model contains 480 residues spread over 80 chains. Does that match what is in your sample? Is it possible that some or all of these amino acids need to be merged into larger polypeptide chain(s)? Perhaps it is not a coincidence that the number of chains is equal to the number of bonds of unrealistic length. Best, Kaspar On Feb 19, 2025, at 2:36 PM, Das, Abhinaba <[email protected]<mailto:[email protected]>> wrote: Thanks Phil and Pavel for pointing it out. The error is likely (I think) of the NH2 ligands not being detected as proper amide linkage. <image002.png> <image001.png> From: Pavel Afonine <[email protected]<mailto:[email protected]>> Date: Wednesday, February 19, 2025 at 2:17 PM To: Das, Abhinaba <[email protected]<mailto:[email protected]>> Cc: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Subject: [External] Re: [ccp4bb] Low atom inclusion score error while depositing to PDB Hi Abhinaba, Here is my interpretation of this… The geometry statistics are overall fine, except for the impossibly bad bond rmsd (overall, and greater than 4σ). This can't be true for an okay model. So I'd stop deposition and check/fix that first! It’s also amazing how one can mess up bond lengths so badly without actually damaging the angles—very interesting! Overall, CCmask suggests the model fits the map okay as a whole. To get a better local picture, you’d need to check values per chain and residue. I wouldn’t worry about the atom inclusion score at all—it’s a pretty meaningless quality metric, and I could spend an hour or two explaining why. Bottom line: Based on the information you’ve supplied, your biggest concern should be bad covalent bonds. Good luck! Pavel On Wed, Feb 19, 2025 at 10:42 AM Das, Abhinaba <[email protected]<mailto:[email protected]>> wrote: Dear Community, I'm trying to deposit an EM volume map and the corresponding model to the PDB. Though validation in Phenix doesn't show anything wrong, the deposition validation indicates a low atom inclusion score. Not sure why the error… Thanks in advance for any insights. <image001.png> <image002.png> <image003.png> ________________________________ 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 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. 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