You can only link a residue (L-peptide) N to another residue (L-peptide) N+1 or N-1 In your case you try to link VAL10 to NLE101… Just change NLE101 to NLE11, then it should work.
> Le 26 oct. 2022 à 03:37, Jiang Xu <foxj...@gmail.com> a écrit : > > 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 > <mailto: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 >> <mailto: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 >> <mailto: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 >>> <mailto: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 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1><change_MET11_to_NLE_101.jpg> ######################################################################## 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/
