File format support: NMRView

Christopher Schulte — Fri, 09 May 2008 14:47:01 -0000

We occasionally get data in NMRView and NMR Pipe formats. Can those be supported?

move issues from todo file to sf.net

jurgenfd — Thu, 03 Apr 2008 14:15:39 -0000

2nr2
reclassify to:
##### BMRB adds: PROGRAM unknown
##### BMRB adds: TYPE order parameter
##### BMRB adds: SUBTYPE n/a
##### BMRB adds: FORMAT n/a

reclassify 2JO8 XEASY chemical shift

2gb8 reclassify to spin label distance restraints in stead of NOE distance restraints

1EZP reclassify to:

##### BMRB adds: PROGRAM XPLOR/CNS
##### BMRB adds: TYPE dipolar coupling
##### BMRB adds: SUBTYPE angle specification
##### BMRB adds: FORMAT n/a

2a55 and 2gd7 have 2 atom RDCs; needs to be improved in parser.

2p7c the discover residue number includes a chain id.
1:TX_7:H5M* 1:LEU_49B:HD11 -1.000 7.0 50.00 50.00 1000.000 0.0
^ bad residue number
It's already fixed in code; just needs to be checked as whole entry.

2jqx SAXS need to be added to the classification.

2o81 Counts 300 138 46.0 same problem as 2p7c
2o83 Counts 284 114 40.1

2jrg Counts 729 504 69.1 await FC update
2jrq Counts 734 578 78.7 await FC update

2jt3 Need to add ambiguous classification for dihedral angle (2edf 2ekx
2el8 2enm)

2hlu Process amber pdb file.
2hlt see 2hlu

2hvu Use new coordinates for the residue 7 and 11 NS1 atoms. Pdb to update.

2p6j Ask authors for decent restraints.

2jtz problem with ligand, update format converter.

2ot2 Redoe Amber parser so the dihedral angle values in the restraints are
remembered from one restraint to the next just as in Amber does that.

2gof Reannotate as per email authors id-ed the data as static dipolar
couplings from ssNMR.

2vah and 2vai Reannotate as CS DIFFERENCE data.

2j52 Reannotate as CS DIFFERENCE data.

2oq3 Process Amber file

2z2g problem with ligand, update format converter.
2z2h problem with ligand, update format converter.

2p4l problem with ligand, update format converter.

2ju4 problem with ligand, RCY. update format converter.

2jpi - large violations with methylenes -update format converter.
This is because all the HB2's are skipped.

2juu get a residue definition for FC for residue ALO.

2jp8 - There is a problem that sometimes happens with atom mapping due to
the PDB remediation. see 2jpi

2jpx remove if authors don't respond (There is no real data, just xml garbage)

2jmh missing protons, large amount restraints did not make to FRED, update format converter.
refer to 2jpi

2rnj see 2jpi

2p80 the xplor pseudocontact program as a restraints file is not an allowed option but
perhaps it should be.

2jya check but JFD pretty certain there are XEASY rdcs.

2jt7 improve discover parser for the distance restraints for this entry.

2jvo improve amber parser for dihedral angles for this entry.
2jvr see 2jvo

2o7w 2o7x 2o7y 2o7z 2o80 2o82
# fc needs to complete sequence in output star file.

2jxm
features needed to be added for data type "Chemical shift perturbation"

2rml
Stereo_assignment don't have correction for the methylene atoms

2ens ambiguous dihedral angles in DYANA (in general).

2rnm ambiguous distances - update CYANA parser.

2jwk, 2jwl - donor and accepter in H Bonds - put on sourceforge

How to run the linker?

jurgenfd — Tue, 11 Mar 2008 14:17:10 -0000

Currently, I'm doing:

set x = 1brv
python -u ~/workspace/recoordD/python/recoord2/msd/getAllInfo.py $x -force

python -u ~/workspace/recoordD/python/recoord2/msd/linkNmrStarData.py $x -noGui -force -raise

But the resulting file: 1brv_linked.str doesn't have the author atoms linked.

See:

loop_
_Dist_constraint.Tree_node_member_constraint_ID
_Dist_constraint.Tree_node_member_node_ID
_Dist_constraint.Contribution_fractional_val
_Dist_constraint.Constraint_tree_node_member_ID
_Dist_constraint.Assembly_atom_ID
_Dist_constraint.Entity_assembly_ID
_Dist_constraint.Entity_ID
_Dist_constraint.Comp_index_ID
_Dist_constraint.Seq_ID
_Dist_constraint.Comp_ID
_Dist_constraint.Atom_ID
_Dist_constraint.Atom_type
_Dist_constraint.Atom_isotope_number
_Dist_constraint.Resonance_ID
_Dist_constraint.Auth_asym_ID
_Dist_constraint.Auth_seq_ID
_Dist_constraint.Auth_comp_ID
_Dist_constraint.Auth_atom_ID
_Dist_constraint.Entry_ID
_Dist_constraint.Distance_constraint_list_ID

1 1 . 1 . . . . . . . . . . 1 171 VALn HB 1 1
1 1 . 2 . . . . . . . . . . 1 171 VALn HN1 1 1
2 1 . 1 . . . . . . . . . . 1 171 VALn HG* 1 1
2 1 . 2 . . . . . . . . . . 1 171 VALn HA 1 1

Recent changes to support-requests

File format support: NMRView

move issues from todo file to sf.net

How to run the linker?