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/
