As Refmac5.8.0349 is used, I am almost sure CCP4 8.0 is used. By the way I would recommend to apply CCP4 update 002 (latest), as a LIBG (base pair/stacking restraints) related bug was fixed in Refmac.
There might be something wrong with 4D4, but the problem is related to OP3 atoms in nucleotides that should not exist, as OP3 atoms should be removed when making phosphodiester bond (p link). This will be fixed by removing them, as Paul pointed out. Best regards, Keitaro On Mon, 18 Jul 2022 at 12:04, Garib Murshadov <ga...@mrc-lmb.cam.ac.uk> wrote: > > That is a strange case. Could you please check the monomer library version? > Especially, could you please check group name for 4D4, there seems to be a > confusion there. > > Regards > Garib > > > On 18 Jul 2022, at 09:28, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > > > On 18/07/2022 07:59, Cryo EM wrote: > >> Hi all, > >> > >> I am working on a pdb of RNA where I intend to change the modified > >> nucleotides to their parent unmodified original residues. For example, PSU > >> to U, 1MG to G and so on. > >> I was wondering if there is a better way to do that by either manually > >> editing the pdb or changing them manually in coot one by one (in Edit: > >> Replace residues)? > > > > > > Sounds hideous. That's what the API is for. > > > > > > (define imol (read-pdb "rna.pdb")) > > > > (let ((mutation-list (list ;; chain-id res-no new/standard-type > > (list "A" 1 "A") > > (list "A" 2 "C") > > (list "A" 3 "G")))) ;; mutate to U seems broken > > > > (for-each (lambda (m) > > > > (let ((chain-id (list-ref m 0)) > > (res-no (list-ref m 1)) > > (new-type (list-ref m 2))) > > > > (mutate-by-overlap imol chain-id res-no new-type))) > > mutation-list)) > > > > You could do something similar in Python. > > > > > >> Despite changing the residues by latter way, there is an error while > >> running servalcat refinement. (attached). > >> > > > > Because of a naive implementation of is-nucleotide? Coot fails to detect > > that the modified nucleotide is a nucleotide and so doesn't delete OP3 for > > you. > > > > From coot-utils.scm: > > > > (if (is-nucleotide? imol chain-id-in resno) > > (if (residue-exists? imol chain-id-in (- resno 1) "") > > (delete-atom imol-ligand "A" 1 "" " OP3" ""))) > > > > You know the residues that need to be replaced, so just loop over them and > > call delete-atom for the "OP3". > > > > > > Paul. > > > > ######################################################################## > > > > 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/ > > ######################################################################## > > 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/ ######################################################################## 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/
