It looks like that it is from ccp4 version 7 series. There, our programs may have changed HN2 with H2. However, you should check if the group name for this entry is L-peptide. If it is not L-peptide then coot will not recognise it as L-peptide (as far as I know)
Regards Garib > On 26 Oct 2022, at 00:18, Jiang Xu <[email protected]> wrote: > > Hi Garib, > Thank you for your help. I looked for NLE in the coot monomer library and > found a file named NLE.cif at '/Applications/ccp4-7.1/lib/data/monomers/n'. I > then searched this file for 'HN2' but didn't find any line that contains this > string. So is it a typo or I was looking at the wrong file? > Sincerely > Jiang > > On Thu, Oct 20, 2022 at 12:36 AM Garib Murshadov <[email protected] > <mailto:[email protected]>> wrote: > 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >> <mailto:[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] >>> <mailto:[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 >>> <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/
