Hi Garib, Thank you for your reply. I edited the NLE.cif file in the CCP4 monomer library. You can see I successfully changed the group to L-peptide, as shown below: /Applications/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif | awk /NLE/ NLE NLE NORLEUCINE L-peptide 22 9 . NLE-D NLE PEPT-D D-NORLEUCINE D-peptide
cat cat /Applications/ccp4-7.1/lib/data/monomers/n/NLE.cif | awk /L-peptide/ NLE NLE NORLEUCINE L-peptide 22 9 . As shown in the following graph, I delete MET11 and then use the "Get monomer" method of Coot using NLE. I then align the NLE to the local electron density. But I couldn't change the linkage type that Coot still regard it not as an a.a. residue but as a small molecule ligand. I also tried to use the "Simple Mutate" tab in Coot to mutate MET11 to NLE, but there's no NLE option there, even after I edited the NLE.cif in the monomer library. So, now the question is how to add the NLE to the Coot "Simple Mutate" list? Do you have any suggestions? Sincerely, Jiang On Tue, Oct 25, 2022 at 4:29 PM Garib Murshadov <ga...@mrc-lmb.cam.ac.uk> wrote: > 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 <foxj...@gmail.com> 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 <ga...@mrc-lmb.cam.ac.uk> > 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 <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> >> 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> 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 >> >> >> > ######################################################################## 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/
