This format requires two input files: residue sequence file and chemical shifts file.
Residue sequence file lists residue labels, one per line, plus optional extra information.
STARch supports two flavours of this format: in plain "XEASY" it uses line number as residue sequence code. Extra columns, if present, are ignored.
GLN LEU THR GLU
"XEASY_N", or "XEASY with sequence numbers" is a variant of the format where sequence file contains residue sequence numbers in second column.
GLN 299 LEU 300 THR 305 GLU 302Use this variant if your residues are not numbered starting from 1.
Sequence file should have extension .seq
Chemical shifts file contains whitespace-separated values, one atom per
line. The order is fixed: ID, shift value, shift value error, atom
name, residue sequence code.
When running STARch from command line, chemical shifts (or "protons") file
must have the same name as sequence file and extension .prot
or .xeasy. Input file name is specified without extension,
STARch will look for .seq file, then for .prot
file, and if it is not found -- for .xeasy file.
Web interface contains separate filename fields for sequence and protons files.
First variant: residue file
GLN LEU THR GLUProtons file:
1 175.75 0.05 C 1 2 54.44 0.05 CA 1 3 8.24 0.05 HN 2 4 4.70 0.05 HA 2 5 0.92 0.05 HG 2 6 177.70 0.05 C 2 7 54.44 0.05 CA 2 8 43.70 0.05 CB 2 9 26.95 0.05 CD1 2 10 23.67 0.05 CD2 2 11 122.88 0.05 N 2 12 0.68 0.05 QD1 2 13 0.93 0.05 QD2 2 14 1.75 0.05 HB2 2 15 1.55 0.05 HB3 2 16 8.66 0.05 HN 3 17 4.54 0.05 HA 3 18 175.60 0.05 C 3 19 60.36 0.05 CA 3 20 70.24 0.05 CB 3 21 21.87 0.05 CG2 3 22 112.76 0.05 N 3 23 1.35 0.05 QG2 3 24 9.03 0.05 HN 4 25 4.03 0.05 HA 4 26 179.59 0.05 C 4 27 60.09 0.05 CA 4 28 29.23 0.05 CB 4 29 36.72 0.05 CG 4 30 120.39 0.05 N 4 31 2.11 0.05 QB 4 32 2.41 0.05 QG 4
loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 GLN H H . . . 2 1 GLN N N . . . 3 1 GLN CA C 54.44 0.05 . 4 1 GLN HA H . . . 5 1 GLN C C 175.75 0.05 . 6 1 GLN CB C . . . 7 1 GLN HB2 H . . . 8 1 GLN HB3 H . . . 9 1 GLN CG C . . . 10 1 GLN HG2 H . . . 11 1 GLN HG3 H . . . 12 1 GLN CD C . . . 13 1 GLN NE2 N . . . 14 1 GLN HE21 H . . . 15 1 GLN HE22 H . . . 16 2 LEU H H 8.24 0.05 . 17 2 LEU N N 122.88 0.05 . 18 2 LEU CA C 54.44 0.05 . 19 2 LEU HA H 4.70 0.05 . 20 2 LEU C C 177.70 0.05 . 21 2 LEU CB C 43.70 0.05 . 22 2 LEU HB2 H 1.75 0.05 . 23 2 LEU HB3 H 1.55 0.05 . 24 2 LEU CG C . . . 25 2 LEU CD1 C 26.95 0.05 . 26 2 LEU HD1 H 0.68 0.05 ? 27 2 LEU CD2 C 23.67 0.05 . 28 2 LEU HD2 H 0.93 0.05 ? 29 2 LEU HG H 0.92 0.05 . 30 3 THR H H 8.66 0.05 . 31 3 THR N N 112.76 0.05 . 32 3 THR CA C 60.36 0.05 . 33 3 THR HA H 4.54 0.05 . 34 3 THR C C 175.60 0.05 . 35 3 THR CB C 70.24 0.05 . 36 3 THR HB H . . . 37 3 THR HG1 H . . . 38 3 THR CG2 C 21.87 0.05 . 39 3 THR HG2 H 1.35 0.05 ? 40 4 GLU H H 9.03 0.05 . 41 4 GLU N N 120.39 0.05 . 42 4 GLU CA C 60.09 0.05 . 43 4 GLU HA H 4.03 0.05 . 44 4 GLU C C 179.59 0.05 . 45 4 GLU CB C 29.23 0.05 . 46 4 GLU HB2 H 2.11 0.05 ? 47 4 GLU HB3 H . . . 48 4 GLU CG C 36.72 0.05 . 49 4 GLU HG2 H 2.41 0.05 ? 50 4 GLU HG3 H . . . 51 4 GLU CD C . . . 52 4 GLU HE2 H . . . stop_
Second variant: residue file
SER 409 ALA 410 GLN 411 ASP 412
1 999.000 0.000 N 409 2 999.000 0.000 HN 409 3 999.000 0.000 CA 409 4 999.000 0.000 HA 409 5 999.000 0.000 CB 409 6 999.000 0.000 HB2 409 7 999.000 0.000 HB3 409 8 999.000 0.000 QB 409 9 999.000 0.000 HG 409 10 170.539 0.000 C 409 11 124.206 0.000 N 410 12 8.670 0.000 HN 410 13 52.618 0.000 CA 410 14 4.351 0.000 HA 410 15 1.380 0.000 QB 410 16 19.252 0.000 CB 410 17 999.000 0.000 HB1 410 18 999.000 0.000 HB2 410 19 999.000 0.000 HB3 410 20 177.138 0.000 C 410 21 119.210 0.000 N 411 22 8.349 0.000 HN 411 23 55.746 0.000 CA 411 24 4.261 0.000 HA 411 25 29.496 0.000 CB 411 26 2.026 0.000 HB2 411 27 1.939 0.000 HB3 411 28 999.000 0.000 QB 411 29 33.737 0.000 CG 411 30 2.341 0.000 HG2 411 31 2.341 0.000 HG3 411 32 999.000 0.000 QG 411 33 999.000 0.000 CD 411 34 111.985 0.000 NE2 411 35 6.822 0.000 HE21 411 36 7.497 0.000 HE22 411 37 999.000 0.000 QE2 411 38 175.403 0.000 C 411 39 121.153 0.000 N 412 40 8.335 0.000 HN 412 41 54.746 0.000 CA 412 42 4.649 0.000 HA 412 43 43.715 0.000 CB 412 44 2.675 0.000 HB2 412 45 2.375 0.000 HB3 412 46 999.000 0.000 QB 412 47 999.000 0.000 CG 412 48 999.000 0.000 HD2 412 49 175.243 0.000 C 412
loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 409 SER H H 999.000 0.000 . 2 409 SER N N 999.000 0.000 . 3 409 SER CA C 999.000 0.000 . 4 409 SER HA H 999.000 0.000 . 5 409 SER C C 170.539 0.000 . 6 409 SER CB C 999.000 0.000 . 7 409 SER HB2 H 999.000 0.000 . 8 409 SER HB3 H 999.000 0.000 . 9 409 SER HG H 999.000 0.000 . 10 409 SER HB2 . 999.000 0.000 ? # Duplicate atom name 11 409 SER HB3 . . . . # Duplicate atom name 12 410 ALA H H 8.670 0.000 . 13 410 ALA N N 124.206 0.000 . 14 410 ALA CA C 52.618 0.000 . 15 410 ALA HA H 4.351 0.000 . 16 410 ALA C C 177.138 0.000 . 17 410 ALA CB C 19.252 0.000 . 18 410 ALA HB H 1.380 0.000 ? 19 410 ALA HB1 . 999.000 0.000 . # Invalid atom 20 410 ALA HB2 . 999.000 0.000 . # Invalid atom 21 410 ALA HB3 . 999.000 0.000 . # Invalid atom 22 411 GLN H H 8.349 0.000 . 23 411 GLN N N 119.210 0.000 . 24 411 GLN CA C 55.746 0.000 . 25 411 GLN HA H 4.261 0.000 . 26 411 GLN C C 175.403 0.000 . 27 411 GLN CB C 29.496 0.000 . 28 411 GLN HB2 H 2.026 0.000 . 29 411 GLN HB3 H 1.939 0.000 . 30 411 GLN CG C 33.737 0.000 . 31 411 GLN HG2 H 2.341 0.000 . 32 411 GLN HG3 H 2.341 0.000 . 33 411 GLN CD C 999.000 0.000 . 34 411 GLN NE2 N 111.985 0.000 . 35 411 GLN HE21 H 6.822 0.000 . 36 411 GLN HE22 H 7.497 0.000 . 37 411 GLN HB2 . 999.000 0.000 ? # Duplicate atom name 38 411 GLN HB3 . . . . # Duplicate atom name 39 411 GLN HG2 . 999.000 0.000 ? # Duplicate atom name 40 411 GLN HG3 . . . . # Duplicate atom name 41 411 GLN QE2 . 999.000 0.000 . # Invalid atom 42 412 ASP H H 8.335 0.000 . 43 412 ASP N N 121.153 0.000 . 44 412 ASP CA C 54.746 0.000 . 45 412 ASP HA H 4.649 0.000 . 46 412 ASP C C 175.243 0.000 . 47 412 ASP CB C 43.715 0.000 . 48 412 ASP HB2 H 2.675 0.000 . 49 412 ASP HB3 H 2.375 0.000 . 50 412 ASP CG C 999.000 0.000 . 51 412 ASP HD2 H 999.000 0.000 . 52 412 ASP HB2 . 999.000 0.000 ? # Duplicate atom name 53 412 ASP HB3 . . . . # Duplicate atom name stop_ ERR::409:SER:Duplicate atom name HB2 ERR::409:SER:Duplicate atom name HB3 ERR::411:GLN:Duplicate atom name HB2 ERR::411:GLN:Duplicate atom name HB3 ERR::411:GLN:Duplicate atom name HG2 ERR::411:GLN:Duplicate atom name HG3 ERR::412:ASP:Duplicate atom name HB2 ERR::412:ASP:Duplicate atom name HB3
Last updated: Fri 02 Jul 2004 05:24:32 PM CDT