STARch input Format3: Nucleic Acid

Table formatted for printout, with each residue occupying one line:

 G1   8.20  n.a.  5.95  4.93  4.71  4.58   12.18 
 C5   7.84  5.67  5.51  4.31  4.45  4.10   8.41   7.00
 A8   7.60  7.64  5.90  4.63  4.55  4.48

This format is very similar to Format 2, except that

with this format you can specify any atom names (Format2 is limited to amino acids),
and all values for one residue must be on one line (in Format2 CA and CB protons may be on the line below).

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 must contain space-separated list of field names. Two field names must be present:

seq_code	residue sequence code
label	Residue label.

The rest are atom names.
Field names are case-insensitive, atom names will be converted to upper case.

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.

Note:

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

10
label seq_code   H8   H2     H1'   H2'   H3'   H4'    im     am
2     3          7    13     19    25    31    37     44     51 
1     3          4    4       4     4    4     4      5      4 
 G1   8.20  n.a.  5.95  4.93  4.71  4.58   12.18 
 C5   7.84  5.67  5.51  4.31  4.45  4.10   8.41   7.00
 A8   7.60  7.64  5.90  4.63  4.55  4.48

STARch output (with residue type set to nucleic acid):

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	G	H8	H	8.20	.	1
2	1	G	H2	H	.	.	.	# shift value=n.a.
3	1	G	"H1'"	H	5.95	.	1
4	1	G	"H2'"	H	4.93	.	1
5	1	G	"H3'"	H	4.71	.	1
6	1	G	"H4'"	H	4.58	.	1
7	1	G	IM	I	12.18	.	1
8	1	G	AM	A	.	.	.	# shift value=null
9	5	C	H8	H	7.84	.	1
10	5	C	H2	H	5.67	.	1
11	5	C	"H1'"	H	5.51	.	1
12	5	C	"H2'"	H	4.31	.	1
13	5	C	"H3'"	H	4.45	.	1
14	5	C	"H4'"	H	4.10	.	1
15	5	C	IM	I	8.41	.	1
16	5	C	AM	A	7.00	.	1
17	8	A	H8	H	7.60	.	1
18	8	A	H2	H	7.64	.	1
19	8	A	"H1'"	H	5.90	.	1
20	8	A	"H2'"	H	4.63	.	1
21	8	A	"H3'"	H	4.55	.	1
22	8	A	"H4'"	H	4.48	.	1
23	8	A	IM	I	.	.	.	# shift value=null
24	8	A	AM	A	.	.	.	# shift value=null
stop_
WARN::1:G:Check atom type: I
WARN::1:G:Check atom type: A
WARN::5:C:Check atom type: I
WARN::5:C:Check atom type: A
WARN::8:A:Check atom type: I
WARN::8:A:Check atom type: A

Last updated: Tue Apr 15 16:09:47 CDT 2003