STARch input Format2

Table formatted for printout, with each residue occupying one or two lines:

Ala1                   51.5 (4.04)    19.1 (1.47)
Glu2         (8.68)    57.1 (4.19)    29.3 (1.90, 1.98) CG 35.3 (2.24)
Gly3   112.6 (8.47)    44.6 (3.81)
                       44.6 (3.94)

For this format you must specify atom names, starting column (offset), and number of columns (length) for each value in file header. When specifying starting columns, keep in mind that TAB is a single character that occupies only one column, whereas 8 consecutive spaces take up 8 columns.

Description

First line may contain number of fields (columns) in the file. This number was required by old version of STARch. Current version does not use this number, but it is supported for backwards compatibility.

Second line (or the first, if the column count is omitted) must contain space-separated list of field names. Field name must be one of the following:

id	residue sequence code
lab	Residue label.
n	Nitrogen.
nh	Nitrogen proton.
co	Carbon.
ca	Alpha carbon.
cb	Beta carbon.
ha1	ca proton 1.
ha2	ca proton 2 if it is stored on the same line as ha1.
+ha2	ca proton 2 if it is stored on line below ha1.
hb1	cb proton 1.
hb2	cb proton 2 if it is stored on the same line as hb1.
+hb2	cb proton 2 if it is stored on line below hb1.
other	Other atoms.

Field names are case-insensitive.
Other field is written out as NMR-STAR comment.

Third line contains field offsets (starting columns), counting from one.

Fourth line contains field lengths. Length of zero means "everything to the end of the line".

Following lines contain values.

Notes:

Do not use TAB as a separator. Although it is usually displayed as 8 spaces on the screen, TAB is in fact a single character that occupies only one column. If you put TABs in the file, column counts will be wrong and STARch will not find the values where it expects them to be. (Unfortunately, TAB is not always 8 spaces: this setting is user-configurable and many editors use e.g. 4 spaces instead of 8 by default. So STARch cannot replace TABs with the right number of spaces because it doesn't know what the right number was when the file was created.)

Example of Format2:

11
lab id n nh ca ha1 +ha2 cb hb1 hb2 other
1   4  8 15 24 30  30   39 45  51  57
3   3  5 4  4  4   4    4  4   4   0
Ala1                   51.5 (4.04)    19.1 (1.47)
Glu2         (8.68)    57.1 (4.19)    29.3 (1.90, 1.98) CG 35.3 (2.24)
Gly3   112.6 (8.47)    44.6 (3.81)
                       44.6 (3.94)

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	1	ALA	H	H	.	.	.
2	1	ALA	N	N	.	.	.
3	1	ALA	CA	C	51.5	.	.
4	1	ALA	HA	H	.	.	.
5	1	ALA	C	C	.	.	.
6	1	ALA	CB	C	19.1	.	.
7	1	ALA	HB	H	.	.	.
8	1	ALA	HA1	.	4.04	.	.	#  Invalid atom
9	1	ALA	HB1	.	1.47	.	.	#  Invalid atom
10	2	GLU	H	H	8.68	.	.
11	2	GLU	N	N	.	.	.
12	2	GLU	CA	C	57.1	.	.
13	2	GLU	HA	H	.	.	.
14	2	GLU	C	C	.	.	.
15	2	GLU	CB	C	29.3	.	.
16	2	GLU	HB2	H	1.98	.	.	# CG 35.3 (2.24)
17	2	GLU	HB3	H	.	.	.
18	2	GLU	CG	C	.	.	.
19	2	GLU	HG2	H	.	.	.
20	2	GLU	HG3	H	.	.	.
21	2	GLU	CD	C	.	.	.
22	2	GLU	HE2	H	.	.	.
23	2	GLU	HA1	.	4.19	.	.	#  Invalid atom
24	2	GLU	HB1	.	1.90	.	.	#  Invalid atom
25	3	GLY	H	H	8.47	.	.
26	3	GLY	N	N	112.6	.	.
27	3	GLY	CA	C	44.6	.	.
28	3	GLY	HA2	H	3.94	.	.
29	3	GLY	HA3	H	.	.	.
30	3	GLY	C	C	.	.	.
31	3	GLY	HA1	.	3.81	.	.	#  Invalid atom
stop_

Last updated: Fri 02 Jul 2004 05:17:45 PM CDT