Hi Xavier, Thank you for your suggestion. Bestt, Jiang On Wed, Oct 26, 2022 at 12:10 AM Xavier Brazzolotto <xbrazzolo...@gmail.com> wrote:
> 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> > 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 > <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/
