Hi, I got the following error when I added a NAG-ASN link in the def file. /nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb Monomer Library directory: "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib" Total number of atoms: 46651 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain S and resname NAG and resid 1001 residue_selection_2: chain A and resname ASN and resid 15 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 46651 Number of chains: 8 Number of residues, atoms: 909, 13713 Unexpected atoms: {'ASN%DEL-HD22,HD22': 1} Classifications: {'peptide': 909} Modifications used: {'DEL-HD22': 1, 'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 601, 8947 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 898, 13559 Classifications: {'peptide': 898} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 602, 8954 Classifications: {'peptide': 602} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 642, 642 Classifications: {'water': 642} Link IDs: {None: 641} Number of residues, atoms: 31, 780 Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23} Classifications: {'undetermined': 31} Modifications used: {'DEL-O1': 1} Link IDs: {None: 30, 'NAG-ASN': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen chiralities: 30 Number of residues, atoms: 16, 16 Unusual residues: {' MG': 2, ' CA': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Number of residues, atoms: 4, 40 Unusual residues: {'IMD': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 " Time building chain proxies: 32.54, per 1000 atoms: 0.70 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Couldn't figure out what went wrong. Can somebody help me? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
Hi Jianghai, The NAG-ASN link is defined with two modifications (in mon_lib_list.cif): NAG-ASN NAG DEL-O1 . ASN DEL-HD22 . bond_NAG-C1_=_ASN-ND2 I haven't looked at the chemistry, but this definition suggests you have to remove the HD22 atom. I.e. remove the corresponding ATOM record from you PDB file. Note that Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 " is formatted exactly like in the PDB file, so you can use this as a search pattern to find the line directly. Ralf
Hi Ralf, This doesn't work. I removed all the H atoms from the pdb file and got the same error. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++ On Oct 6, 2007, at 10:40 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
The NAG-ASN link is defined with two modifications (in mon_lib_list.cif):
NAG-ASN NAG DEL-O1 . ASN DEL-HD22 . bond_NAG-C1_=_ASN-ND2
I haven't looked at the chemistry, but this definition suggests you have to remove the HD22 atom. I.e. remove the corresponding ATOM record from you PDB file. Note that
Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 "
is formatted exactly like in the PDB file, so you can use this as a search pattern to find the line directly.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
If it is showing you this line
"HD22 ASN A 15 "
this must be in the PDB file. I cannot come from anywhere else. Maybe it is reading a different PDB file than you think? Are you using a .def file, or are you specifying the pdb file on the command line? If you think that's not it, move the pdb file you think it is reading somewhere else, then try again. If it stops because it cannot find the file, move it back. If it works then, shows the line above, but the corresponding ATOM card is not in the PDB file, then I wouldn't know how that could be. :-) Ralf
Hi Ralf, I now know what happened. When reduce adds H atoms into the pdb file, it finds the glycosylation bonds between NAG and ASN. There are two H atoms attached to the ND2 of ASN and reduce deletes the H atom named HD21 and keeps HD22. However, in the mon_lib_list.cif, the library wants to delete the other H atom named HD22 and keep HD21. That's where this error came from. So if I change the HD22 to HD21, everything is fine. If I delete HD22, it is fine too. I have a lot of glycans and it is very tedious to manually change HD22 to HD21 or delete HD22 one by one in the pdb file. Could you please fix this? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++ On Oct 6, 2007, at 10:40 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
The NAG-ASN link is defined with two modifications (in mon_lib_list.cif):
NAG-ASN NAG DEL-O1 . ASN DEL-HD22 . bond_NAG-C1_=_ASN-ND2
I haven't looked at the chemistry, but this definition suggests you have to remove the HD22 atom. I.e. remove the corresponding ATOM record from you PDB file. Note that
Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 "
is formatted exactly like in the PDB file, so you can use this as a search pattern to find the line directly.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thanks for reporting this problem! While we work on a fix, you can easily patch your PDB files like this: sed 's/HD22 ASN/HD21 ASN/' good.pdb > better.pdb Ralf
There is a little problem here. The ASN residues which are not glycosylation sites have both HD21 and HD22. If I simply replace HD22 with HD21, those ASN residues will have two HD21 atoms. So it is more complicated than one line sed script. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++ On Oct 7, 2007, at 12:20 PM, Ralf W. Grosse-Kunstleve wrote:
Thanks for reporting this problem! While we work on a fix, you can easily patch your PDB files like this:
sed 's/HD22 ASN/HD21 ASN/' good.pdb > better.pdb
Ralf
grep -v 'HD21 ASN' good.pdb | sed 's/HD22 ASN/HD21 ASN/' > better.pdb Do you have multiple conformations? Then it would be slightly more tricky (but still easy). Ralf
participants (2)
-
Jianghai Zhu -
Ralf W. Grosse-Kunstleve