Experimental domain structures:
This option is used to provide the experimental domain structures if some of them are available.
The file should be prepared in the following format:
def:1-65;66-143;144-230;
dom:66-143
ATOM 520 N GLU A 66 25.585 40.127 -0.472 1.00 0.00
ATOM 521 CA GLU A 66 25.017 38.857 -0.010 1.00 0.00
ATOM 522 C GLU A 66 24.308 39.045 1.325 1.00 0.00
ATOM 523 O GLU A 66 23.285 38.479 1.670 1.00 0.00
...
ATOM 1133 N GLU A 143 10.161 20.719 -0.357 1.00 0.00
ATOM 1134 CA GLU A 143 9.315 19.633 -0.806 1.00 0.00
ATOM 1135 C GLU A 143 9.694 19.246 -2.237 1.00 0.00
ATOM 1136 O GLU A 143 10.347 20.026 -2.931 1.00 0.00
dom:144-230
ATOM 1142 N PRO A 144 9.275 18.060 -2.646 1.00 0.00
ATOM 1143 CA PRO A 144 9.549 17.539 -3.976 1.00 0.00
ATOM 1144 C PRO A 144 8.946 18.494 -4.997 1.00 0.00
ATOM 1145 O PRO A 144 7.960 19.146 -4.633 1.00 0.00
...
ATOM 1771 N VAL A 230 -3.010 30.415 -21.695 1.00 0.00
ATOM 1772 CA VAL A 230 -3.900 29.255 -21.558 1.00 0.00
ATOM 1773 C VAL A 230 -3.594 28.233 -22.648 1.00 0.00
ATOM 1774 O VAL A 230 -3.677 28.584 -23.844 1.00 0.00
The file starts with the domain definition of the query sequence in the first line
(
blue). The domain definition must start with "def:", and
a domain or a segment should be represented by a start residue index and an end residue
index with "-" in the middle, e.g., "1-65". The domains should be separated
by semicolons, e.g., "1-65;66-143;". For the discontinuous domain wich has multiple
segments, the segments should be separated by commas, e.g., "227-256,386-420;". The
length of a domain should be between 30 and 1000. All residue indexes should be
included in the definition. Any loss or overlap of residue indexes will result in the error.
For example, "1-99;101-226;227-256;" is
not allowed as residue 100 is missed. In addition, please make sure the definition is
written on one line and ends with a semicolon. The last semicolon cannot be missed.
The provided experimental domain model information starts from the second line.
The residue index range (
red) of the domain should be written in
the first line in this part and starts with "dom:". The range should be same with that
in the domain definition (
blue). In the example, "66-143" indicates
the first provded domain is from residue 66 to 143. The domain structure with
standard PDB information is written below this line until the information of
the second provided domain, which starts from "dom:144-230" (
green)
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