I hope this doesn't confuse the discussion, but my understanding was "UNK" stood for "unknown" residue and this will cause errors. UNK naming convention is the default output of Schrodinger when generating ligand PDB files. Coot will display the PDB containing "UNK" as a residue, but if you try to use the CIF file to real-space refine, the ligand will blow up. I found that renaming the residue in the output PDB and regenerating the CIF file with the corrected RESID name solved the problem. So in my experience, the problem is the name "UNK" and this just needs to be switched to something else. Has anyone else seen this? Nick
On Sat, Feb 13, 2021 at 4:29 PM Tristan Croll <ti...@cam.ac.uk> wrote: > Browsing backwards through a dozen or so of the most recent UNK-containing > structures, I haven't found a counter-example yet - apart from those where > the UNK residues are a single contiguous stretch and given their own chain > ID. So a recent problem? > ------------------------------ > *From:* Philip D. Jeffrey <pjeff...@princeton.edu> > *Sent:* 12 February 2021 19:56 > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>; Tristan Croll < > ti...@cam.ac.uk> > *Subject:* Re: Bug in mmCIF handling of UNK residues? > > Doesn't seem to be the case for all instances: that table isn't present in > 5BV0 despite the N-terminal residues of Nyv1 being modeled as UNK in the > Vps16:Vps33:Nyv1 complex due to a symmetry overlap. Nyv1, C165-179 are UNK > with partial occupancy, which is the N-terminal part of the model for that > chain, then there's a gap of 3 missing residues, and then there's > polypeptide model which we've assigned to sequence, all in the same chain. > > Not sure if the missing table is something that turned up after the > deposition date (June 2015), or if it's related to the missing residues > between the UNK segment and the defined amino acids. > > Phil Jeffrey > Princeton > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tristan > Croll <ti...@cam.ac.uk> > *Sent:* Friday, February 12, 2021 1:03 PM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] Bug in mmCIF handling of UNK residues? > > Hi all, > > If I open (as far as I can tell) the mmCIF for any structure in the wwPDB > that contains both defined amino acids and UNK in the same chain, then the > UNK section is treated as covalently bonded to the flanking sequence. This > appears to be a bug in the mmCIF generation itself, not in the viewing > software (ChimeraX, in this case): if I look in 7kzn as a random example, I > see: > > loop_ > _pdbx_validate_polymer_linkage.id > _pdbx_validate_polymer_linkage.PDB_model_num > _pdbx_validate_polymer_linkage.auth_atom_id_1 > _pdbx_validate_polymer_linkage.auth_asym_id_1 > _pdbx_validate_polymer_linkage.auth_comp_id_1 > _pdbx_validate_polymer_linkage.auth_seq_id_1 > _pdbx_validate_polymer_linkage.PDB_ins_code_1 > _pdbx_validate_polymer_linkage.label_alt_id_1 > _pdbx_validate_polymer_linkage.auth_atom_id_2 > _pdbx_validate_polymer_linkage.auth_asym_id_2 > _pdbx_validate_polymer_linkage.auth_comp_id_2 > _pdbx_validate_polymer_linkage.auth_seq_id_2 > _pdbx_validate_polymer_linkage.PDB_ins_code_2 > _pdbx_validate_polymer_linkage.label_alt_id_2 > _pdbx_validate_polymer_linkage.dist > 1 1 C X UNK 345 ? ? N X UNK 348 ? ? 10.08 > 2 1 C X UNK 396 ? ? N X UNK 403 ? ? 28.65 > 3 1 C Y UNK 281 ? ? N Y UNK 284 ? ? 6.72 > 4 1 C Y UNK 387 ? ? N Y UNK 394 ? ? 22.26 > 5 1 C Y UNK 420 ? ? N Y UNK 424 ? ? 12.82 > > Considering that the coords themselves generally seem fine, I guess this > is happening post deposition? > > Best regards, > > Tristan > > ------------------------------ > > 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 > -- Nick Larsen Director - Lead Discovery H3 Biomedicine | an Eisai Oncology Company 300 Technology Sq #5 Cambridge, MA 02139 https://www.h3biomedicine.com/ -- [This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.] ######################################################################## 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/
