STARch input Format4

This is a generic input format, where each line contains data for one residue and values are separated by whitespace (spaces and/or tabs). Many spreadsheet programs, such as Microsoft Excel, can export data in this format (often called "tab-delimited" file).

The difference between this format and Format1 is that in Format1 each atom occupies one line, and you can specify atom type, chemical shift value error and ambiguity code. In Format4 each residue occupies one line, atom names are column headers, and you can only specify chemical shift values.

Each line must contains residue sequence number and residue label, plus any number of chemical shift values.

To convert this format, you will need to add column headers in the first line of the file. Column headers other than the first two (residue label and number) are atom names, they are converted to uppercase in STARch output (but otherwise are unchanged). Make sure to put non-blank character(s) (e.g. a dash, or "n/a") in place of missing values.

Description

First line must contain space-separated list of field names. First two field names must be:

seq_code	Sequence code of the residue
label	Residue label.

Note that these two columns must be the first columns in the file.
The rest are atom names.
Field names are case-insensitive.

Following lines contain space-separated field values, one residue per line.

Note that you must put something (e.g. a dash or "n/a") in place of missing values, unless it's in the last (rightmost) column.

Example

label	seq_code	hn	N	CO	CA	CB
TYR	157	9.163	128.376	175.04	53.236	39.168
PRO	158	n/a	n/a	179.933	59.472	29.883
TRP	159	9.08	124.828	173.979	56.268	26.557
LEU	173	7.241	120.238	177.6	50.63	40.693

STARch output (with residue type set to 20 common amino acids):

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	157	TYR	H	H	9.163	.	.
2	157	TYR	N	N	128.376	.	.
3	157	TYR	CA	C	53.236	.	.
4	157	TYR	HA	H	.	.	.
5	157	TYR	C	C	175.04	.	.
6	157	TYR	CB	C	39.168	.	.
7	157	TYR	HB2	H	.	.	.
8	157	TYR	HB3	H	.	.	.
9	157	TYR	CG	C	.	.	.
10	157	TYR	CD1	C	.	.	.
11	157	TYR	HD1	H	.	.	.
12	157	TYR	CD2	C	.	.	.
13	157	TYR	HD2	H	.	.	.
14	157	TYR	CE1	C	.	.	.
15	157	TYR	HE1	H	.	.	.
16	157	TYR	CE2	C	.	.	.
17	157	TYR	HE2	H	.	.	.
18	157	TYR	CZ	C	.	.	.
19	157	TYR	HH	H	.	.	.
20	158	PRO	N	N	.	.	.	# shift.val = n/a
21	158	PRO	CA	C	49.472	.	.
22	158	PRO	HA	H	.	.	.
23	158	PRO	C	C	179.933	.	.
24	158	PRO	CB	C	29.883	.	.
25	158	PRO	HB2	H	.	.	.
26	158	PRO	HB3	H	.	.	.
27	158	PRO	CG	C	.	.	.
28	158	PRO	HG2	H	.	.	.
29	158	PRO	HG3	H	.	.	.
30	158	PRO	CD	C	.	.	.
31	158	PRO	HD2	H	.	.	.
32	158	PRO	HD3	H	.	.	.
33	158	PRO	H	.	.	.	.	# shift.val = n/a  Invalid atom
34	159	TRP	H	H	9.08	.	.
35	159	TRP	N	N	124.828	.	.
36	159	TRP	CA	C	56.268	.	.
37	159	TRP	HA	H	.	.	.
38	159	TRP	C	C	173.979	.	.
39	159	TRP	CB	C	26.557	.	.
40	159	TRP	HB2	H	.	.	.
41	159	TRP	HB3	H	.	.	.
42	159	TRP	CG	C	.	.	.
43	159	TRP	CD1	C	.	.	.
44	159	TRP	HD1	H	.	.	.
45	159	TRP	CD2	C	.	.	.
46	159	TRP	NE1	N	.	.	.
47	159	TRP	HE1	H	.	.	.
48	159	TRP	CE2	C	.	.	.
49	159	TRP	CE3	C	.	.	.
50	159	TRP	HE3	H	.	.	.
51	159	TRP	CZ2	C	.	.	.
52	159	TRP	HZ2	H	.	.	.
53	159	TRP	CZ3	C	.	.	.
54	159	TRP	HZ3	H	.	.	.
55	159	TRP	CH2	C	.	.	.
56	159	TRP	HH2	H	.	.	.
57	173	LEU	H	H	7.241	.	.
58	173	LEU	N	N	120.238	.	.
59	173	LEU	CA	C	50.63	.	.
60	173	LEU	HA	H	.	.	.
61	173	LEU	C	C	177.6	.	.
62	173	LEU	CB	C	40.693	.	.
63	173	LEU	HB2	H	.	.	.
64	173	LEU	HB3	H	.	.	.
65	173	LEU	CG	C	.	.	.
66	173	LEU	CD1	C	.	.	.
67	173	LEU	HD1	H	.	.	.
68	173	LEU	CD2	C	.	.	.
69	173	LEU	HD2	H	.	.	.
70	173	LEU	HG	H	.	.	.
stop_

Last updated: Fri 02 Jul 2004 05:18:35 PM CDT