Selecting residue type

Selecting residue type turns on or off nomenclature conversion and error checking code in STARch.

Web interface has radio buttons for residue types STARch knows about.

When using command line interface, run STARch with -hresidues argument to see the list of known residue types (numbers). To specify residue type on command line, use -r NUM (where NUM is residue type number) parameter.

Residue types and atom nomenclature conversions

20 common amino-acids

For this residue type, STARch will attempt to

convert 1-letter residue labels to 3-letter ones,
add atom types if not present in input,
add chemical shift ambiguity codes if not present in input, and atom has chemical shift value,
add records for all atoms in the residue, not just for those present in input,
flag invalid atoms.

nucleic acid

a warning message is printed if atom type (1^st character of atom name) is not one of N, C, H, or P.

other

Turns off all atom name checks/conversions. Command-line equivalent: omit the -r parameter.

Example of nomenclature conversions (20 common amino-acids)
Input records:

3	LYS	HB+	1.49
3	LYS	QG	1.10
3	LYS	QD	1.55
3	LYS	QE	2.89
4	HIS	CA	53.95

Output without conversions:

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	3	LYS	HB+	.	1.49	.	1
2	3	LYS	QG	.	1.10	.	1
3	3	LYS	QD	.	1.55	.	1
4	3	LYS	QE	.	2.89	.	1
5	4	HIS	CA	.	53.95	.	1
stop_

Output with conversions:

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	3	LYS	H	H	.	.	.
2	3	LYS	N	N	.	.	.
3	3	LYS	CA	C	.	.	.
4	3	LYS	HA	H	.	.	.
5	3	LYS	C	C	.	.	.
6	3	LYS	CB	C	.	.	.
7	3	LYS	HB2	H	.	.	.
8	3	LYS	HB3	H	.	.	.
9	3	LYS	CG	C	.	.	.
10	3	LYS	HG2	H	1.10	.	2
11	3	LYS	HG3	H	.	.	.
12	3	LYS	CD	C	.	.	.
13	3	LYS	HD2	H	1.55	.	2
14	3	LYS	HD3	H	.	.	.
15	3	LYS	CE	C	.	.	.
16	3	LYS	HE2	H	.	.	.
17	3	LYS	HE3	H	.	.	.
18	3	LYS	NZ	N	.	.	.
19	3	LYS	HZ	H	2.89	.	1
20	3	LYS	HB+	.	1.49	.	1	# Invalid atom
21	4	HIS	H	H	.	.	.
22	4	HIS	N	N	.	.	.
23	4	HIS	CA	C	53.95	.	1
24	4	HIS	HA	H	.	.	.
25	4	HIS	C	C	.	.	.
26	4	HIS	CB	C	.	.	.
27	4	HIS	HB2	H	.	.	.
28	4	HIS	HB3	H	.	.	.
29	4	HIS	CG	C	.	.	.
30	4	HIS	ND1	N	.	.	.
31	4	HIS	HD1	H	.	.	.
32	4	HIS	CD2	C	.	.	.
33	4	HIS	HD2	H	.	.	.
34	4	HIS	CE1	C	.	.	.
35	4	HIS	HE1	H	.	.	.
36	4	HIS	NE2	N	.	.	.
37	4	HIS	HE2	H	.	.	.
stop_

Last updated: Fri Jan 3 15:00:23 CST 2003