ROSETTA formats for NMR data (RosettaNMR-v2_0) ********************************************* chemical shifts 1 line per residue format(a3,1x,i4,7(1x,f7.2)) AA (1 letter or 3 letter), residue number, chem shifts (C,CA,CB,HA,N) any unknown shifts should be '9999.00' The sample file below also has the actual phi and psi as the last two fields on the line. These aren't read in; they can be present or absent ------- 1d3z_.chsft_in ----------- M 1 170.54 54.45 33.27 4.23 9999.00 180.00 -180.00 Q 2 175.92 55.08 30.76 5.25 123.22 -91.02 138.26 I 3 172.45 59.57 42.21 4.21 115.34 -131.09 163.04 F 4 175.32 55.21 41.48 5.63 118.11 -115.99 140.22 V 5 174.87 60.62 34.23 4.72 121.00 -118.03 114.22 (etc) ---------------------------------- ********************************************* NOE constraint file format: car comment car comment car comment car n_pairLines (# of lines of constraints to read) car tag,res1,atom1,res2,atom2,upperbound,lowerbound,{true distance} car car format(a1,2x,i4,1x,a4,1x,i4,1x,a4,1x,f10.2,1x,f10.2) car tag: '#':ignore,(actually any non-whitespace char) car true distance is optional and not read car atom1 and atom2 should follow pdb-style atom names with IUPAC numbering car also allowed: ' CEN' for centroid constraints (not evaluted in fullatom mode) car degenerate hydrogen references allowed (no degenerate heavy atoms) res1 and res2 are residue numbers atom names should be in the pdb format ie ' CA ', ' CG ' etc. left justified names are likely okay. Hydrogen atom names should follow the PDB convention (eg. LEU HB atoms are '1HB ' and '2HB '). A complete list of atom names is given in the file read_aaproperties.f. Use the '-IUPAC' option to switch to IUPAC-style hydrogen numbering (ie LEU HB atom are '2HB ' and '3HB '). Degenerate hydrogens attached to the same heavy atom are allowed (eg. LEU HB can be '#HB '). These restraints are evaluated using the heavy atom coordinates and the upper bound is padded by 1.3A (degenerate_padding parameter in distConstraint.h). 'CEN' is also a valid atom name. This is a constraint between sidechain centroids for use in early rosetta phases before fullatom representation of sidechains. If you do not include CEN constraints, but have constraints between sidechain atoms, CEN constraints will be automatically generated. -------1d3z_.cst------------------------------ RosettaNMR-v2_0 compliant HA-H csts, subset from 1d3z.mr PDB deposition data set used in Bowers et al., (2000) J Biomol NMR 18:311 55 6 H 68 HA 3.71 0.00 2.23 5 HA 67 H 3.79 0.00 2.27 3 HA 64 H 3.92 0.00 2.35 4 H 66 HA 3.94 0.00 2.36 22 HA 56 H 4.31 0.00 2.58 (etc) -------------------------------------------- ********************************************** Dipolar constraints: car file format: car line1: comments car line2: comments car line3: comments car line4: # of lines to read (<=physical number of lines) car line5 -> beginning in 1st column car tag res1 atom1 res2 atom2 J car a1 2x i4 1x a4 ix a4 1x 4x 1x f10.2 car car 200 format(a1,2x,i4,1x,a4,1x,i4,1x,a4,1x,f10.2) car car if the first character of a line is '#', the line is read, but car the data is ignored. car otherwise, the first column of each line contains a tag identifying car the set to which the measurement belongs. (ie different experimental car conditions with different alignment tensor) tags may be any car single character other than '#' car ------------------------------------------------------------------------------- sample data file > everything over here is just my comments > and shouldn't be in the file ------------------------------------------------------------------------ 1d3z (662 total) comments JACS 1998 120:12334 comments Ottiger & Bax, H & HA only (134) comments 134 lines to read (include '#' lines) a 2 N 2 H -8.17 a 3 N 3 H 8.27 H-N data, a is a tag a 4 N 4 H 10.49 # 5 N 5 H 9.87 commented out line a 6 N 6 H 9.15 a 7 N 7 H 3.70 .... (lots more lines) a 2 CA 2 HA 5.60 a 3 CA 3 HA 8.98 HA-CA data, same conditions a 4 CA 4 HA 24.27 (ie alignment tensor) as a 5 CA 5 HA 21.73 HN data above a 6 CA 6 HA 16.15 (etc) --------------------------------------------------------------------- ************************************************************************@