![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#2483 closed defect (nonchimerax)
mmCIF linking issues
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
If I save a mmCIF file with disulfides and N-linked glycans from ChimeraX, run it through phenix.refine and load the resulting mmCIF back into ChimeraX, the disulfides and Asn-NAG bonds are gone but the sugar-sugar glycosidic bonds are preserved. Looking at the _struct_conn loop for both files, it's not really clear to me why this should be:
File saved from ChimeraX (reloads with correct linking):
loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_dist_value disulf1 disulf SG . A 2 A 31 ? CYS 1_555 SG . B 188 B 340 ? CYS 1_555 2.029 disulf2 disulf SG . B 236 B 388 ? CYS 1_555 SG . B 240 B 392 ? CYS 1_555 2.012 disulf3 disulf SG . C 2 C 31 ? CYS 1_555 SG . D 189 D 340 ? CYS 1_555 2.011 disulf4 disulf SG . D 237 D 388 ? CYS 1_555 SG . D 241 D 392 ? CYS 1_555 2.032 covale1 covale O4 . E . D 1000 ? NAG 1_555 C1 . F . D 1001 ? NAG 1_555 1.466 covale2 covale O4 . G . D 1010 ? NAG 1_555 C1 . H . D 1011 ? NAG 1_555 1.456 covale3 covale O4 . H . D 1011 ? NAG 1_555 C1 . I . D 1012 ? BMA 1_555 1.448 covale4 covale O3 . I . D 1012 ? BMA 1_555 C1 . L . D 1015 ? MAN 1_555 1.446 covale5 covale O6 . I . D 1012 ? BMA 1_555 C1 . J . D 1013 ? MAN 1_555 1.456 covale6 covale O3 . J . D 1013 ? MAN 1_555 C1 . K . D 1014 ? MAN 1_555 1.466 covale7 covale ND2 . D 135 D 286 ? ASN 1_555 C1 . E . D 1000 ? NAG 1_555 1.448 covale8 covale ND2 . D 108 D 259 ? ASN 1_555 C1 . G . D 1010 ? NAG 1_555 1.447
File written by Phenix (only glycosidic bonds are formed):
loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_auth_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_role _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_auth_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_role _struct_conn.details C00001 disulf CYS A 31 SG CYS A 31 SG . CYS B 340 SG CYS B 340 SG . 'Comput. Cryst. Newsl. (2015), 6, 13-13.' C00002 disulf CYS B 388 SG CYS B 388 SG . CYS B 392 SG CYS B 392 SG . 'Comput. Cryst. Newsl. (2015), 6, 13-13.' C00003 disulf CYS C 31 SG CYS C 31 SG . CYS D 340 SG CYS D 340 SG . 'Comput. Cryst. Newsl. (2015), 6, 13-13.' C00004 covale ASN D 259 ND2 ASN D 259 ND2 . NAG D 1010 C1 NAG D 1010 C1 . 'Taken from Monomer Library or GeoStd' C00005 covale ASN D 286 ND2 ASN D 286 ND2 . NAG D 1000 C1 NAG D 1000 C1 . 'Taken from Monomer Library or GeoStd' C00006 disulf CYS D 388 SG CYS D 388 SG . CYS D 392 SG CYS D 392 SG . 'Comput. Cryst. Newsl. (2015), 6, 13-13.' C00007 covale MAN D 1014 C1 MAN D 1014 C1 . MAN D 1013 O3 MAN D 1013 O3 . 'Bond created based on atom type and distance.' C00008 covale MAN D 1015 C1 MAN D 1015 C1 . BMA D 1012 O3 BMA D 1012 O3 . 'Bond created based on atom type and distance.' C00009 covale BMA D 1012 C1 BMA D 1012 C1 . NAG D 1011 O4 NAG D 1011 O4 . 'Bond created based on atom type and distance.' C00010 covale BMA D 1012 O6 BMA D 1012 O6 . MAN D 1013 C1 MAN D 1013 C1 . 'Bond created based on atom type and distance.' C00011 covale NAG D 1000 O4 NAG D 1000 O4 . NAG D 1001 C1 NAG D 1001 C1 . 'Bond created based on atom type and distance.' C00012 covale NAG D 1010 O4 NAG D 1010 O4 . NAG D 1011 C1 NAG D 1011 C1 . 'Bond created based on atom type and distance.'
Will attach the actual files.
Attachments (2)
Change History (4)
by , 6 years ago
| Attachment: | working_noh.cif added |
|---|
comment:1 by , 6 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
The bug is in the Phenix struct_conn table. In there, for NAG, the ptnr[12]_label_seq_id is different than the label_seq_id in the atom_site table. No match, no bond. For atom_site.label_seq_id it is '.' and in the struct_conn table it appears to be using the atom_site.auth_seq_id value.
The error in the struct_conf table might be related. It appears that atom_site.auth_seq_id values are being used for the struct_conf_{beg,end}_label_seq_id values.
The label_* fields are used to uniquely identify atoms (except for solvent, where the PDB broke the database paradigm -- don't get me started). The auth_* fields can be anything the author wanted and thus are ignored when generating connectivity.
You need to file a bug with the Phenix folks.
File saved by ChimeraX