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 <[email protected]> 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 <[email protected]> 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 > > > ######################################################################## 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/
