If you import cif dictionary then in coot mutate residue should work. At least it worked n one of our problematic cases. If it does not work then Paul Emsley may be able to help.
Regards Garib > On 20 Oct 2022, at 02:06, Jiang Xu <foxj...@gmail.com> wrote: > > 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/
