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data:cathdomall [2008/09/08 16:40] – created sillitoedata:cathdomall [2015/09/30 16:31] (current) – sillitoe
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 +====== Cath Domall File (CDF) ======
 +
 +===== Version 2.0 =====
 +
 +The CATH Domall file describes domain boundaries for entries in the CATH database. 
 +All PDB chains in CATH that contain 1 or more domains have a CathDomall entry. Whole
 +chain domains can be identified where the number of domains is 1 and the
 +number of fragments is 0.
 +
 +  * Comment lines start with a '#' character
 +  * Segments are continuous sequence regions of domains
 +  * Fragments are small regions of the protein chain that are excluded from the domain definition
 +
 +^ Column ^ Description ^
 +| 1  | Chain name (5 characters)  |
 +| 2  | Number of domains (formatted 'D%02d')  |
 +| 3  | Number of fragments (formatted 'F%02d')  |
 +
 +
 +The formatting of a Cath Domall file is best explained using examples.
 +
 +===== Example Domall Entries =====
 +
 +<code>
 +KEY:
 +N  = Number of segments
 +C  = Chain character
 +I  = Insert character/code ('-' indicates no insert character)
 +S  = Start PDB number
 +E  = End PDB number
 +NR = number of residues (fragment information only)
 +</code>
 +
 +==== Example 1 ====
 +
 +
 +<code>
 +1chmA  D02 F00  1  A 2 - A  156 -  1  A  157 - A  402 -
 + N |C S I C E I| N |C    S I C    E I|
 +               |<----Domain One---->|<-----Domain Two---->|
 +                  |<--Segment One-->|   |<--Segment One-->|
 +</code>
 +
 +This translates to:
 +
 +^ Domain   ^ Chain  ^ Start/Stop  ^
 +| 1chmA01  | A      | 2-156     |
 +| 1chmA02  | A      | 157-402   |
 +
 +==== Example 2 ====
 +
 +<code>
 +1cnsA  D02 F00  2  A    1 - A   87 -  A  146 - A  243 -  1  A   88 - A  145 -
 +
 +                N |C    S I C    E I| C    S I C    E I| N |C    S I C    E I|
 +               |<--------------Domain One------------->|<-----Domain Two---->|
 +                  |<--Segment One-->|<---Segment Two-->|   |<--Segment One-->|
 +</code>
 +
 +This translates to:
 +
 +^ Domain   ^ Chain  ^ Start/Stop  ^
 +| 1cnsA01  | A      | 1-87, 146-243  |
 +| 1cnsA02  | A      | 88-145        |
 +
 +
 +===== Fragment Information =====
 +
 +Fragments are small regions of the protein chain that are not included
 +in the domain definition. These residue ranges are tagged on the end of the
 +segment information. The format is different from the segment range information.
 +
 +==== Example 3 ====
 +
 +
 +<code>
 +1amg 0 D02 F01  1  0 1 - 0  360 -  1  0  362 - 0  417 -  0  361 - 0  361 - (1)
 + N |C S I C E I| N |C    S I C    E I| C S I C    E I  NR|
 +               |<----Domain One---->|<-----Domain Two---->|<---Fragment One----->|
 +                  |<--Segment One-->|   |<--Segment One-->|
 +</code>
 +
 +This translates to:
 +
 +^ Domain   ^ Chain  ^ Start/Stop  ^
 +| 1amg001   | A  | 1-360    |
 +| 1amg002   | A  | 362-417  |
 +
 +Fragment = 361
 +
 +==== Example 4 ====
 +
 +<code>
 +1bcmA  D02 F02  1  A  257 - A  487 -  1  A  492 - A  559 -  A  488 - A  491 - (4)  A  560 - A  560 - (1)
 + N |C S I C E I| N |C    S I C    E I| C S I C    E I  NR| C S I C E I  NR|
 +               |<----Domain One---->|<-----Domain Two---->|<---Fragment One----->|<---Fragment Two----->|
 +                  |<--Segment One-->|   |<--Segment One-->|
 +</code>
 +
 +This translates to:
 +
 +^ Domain   ^ Chain  ^ Start/Stop  ^
 +| 1bcmA01  | A  | 257-487  |
 +| 1bcmA02  | A  | 492-559  |
 +
 +Fragments = 488-491, 560
  

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