Hi Jiang, It could have a lot of causes. What I would first check is that the chainID of the NLE is the same as from the surrounding protein, that the new NLE has the same residue number as the deleted MET. I would also check that the position within the coordinate file is the same as the previous MET.
Good luck! Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Jiang Xu Gesendet: Donnerstag, 20. Oktober 2022 03:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] mutate Methionine to Norleucine in Coot. Hi Garib, I deleted the Met residue and imported the nle.cif file into the dictionary and checked the "create a molecule" box.I then used "real space refinement" to align it correctly with the electron density. I then save the merged molecule as a new pdb file but when I reopened the new file, I found the NLE molecule's position was not aligned with the electron density and couldn't be corrected with "real space refinement" in Coot. So any suggestions? Thank you, Best, Jiang On Wed, Oct 19, 2022 at 12:44 PM Garib Murshadov <ga...@mrc-lmb.cam.ac.uk<mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: NLE is in the monomer library. However, it is marked as non-polymer. The reason why it is non-polymer is that one of the hydrogen atoms on N is called HN2 (in peptides they are H, H2 and H3). One easy way would be replace HN2 with H and save in a cif file. Then read it in coot using “import cif dictionary" and hope that coot will recognise it as peptide. I attach nle.cif just in case Regards Garib On 19 Oct 2022, at 20:34, Jiang Xu <foxj...@gmail.com<mailto:foxj...@gmail.com>> wrote: Hello Guys, I have a question regarding how to change the standard amino acid in my structure to Norleucine. It turned out that the one Methionine should be Norleucine. I tried to use the coot's mutation method but didn't find NLE(Norleucine) there. Any suggestions? Thank you, Best, Jiang Lin Chen Lab University of Southern California ________________________________ 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://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<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/
