Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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104<br />
Chapter 11: Command Syntax<br />
Table 11.8. Keywords syntax for ska input file<br />
Keyword syntax Mode Description<br />
MODE mode all The SKA operating mode; allowed values are:<br />
*align*: structurally align two or more protein structures<br />
to on another. This is the default mode<br />
*scan*: given a query structure scan a database of protein<br />
structures and identify potential structural homologues<br />
*dbcreate*: create a database that can be search in<br />
scan mode from a list of PDB files<br />
QUERY_FILE filename<br />
[name]<br />
TEMPLATE filename<br />
[name]<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong><br />
*align*<br />
*scan*<br />
Required. The input query structure. In *align* mode,<br />
the structure against which other proteins are aligned. In<br />
*scan* mode, the structure used for scanning the database.<br />
The optional name (*align* mode only) sets the<br />
name of this structure to a value other than the filename<br />
(the default). The name is displayed in the output file<br />
(see Examples, below). name cannot contain the file separator<br />
character (‘/’ on UNIX).<br />
*align* Required. PDB structures that are to be aligned to the<br />
query structure, set by QUERY_FILE. The TEMPLATE<br />
keyword can appear multiple times in order to be able to<br />
carry out multiple structure alignments (aligning more<br />
than one template structure to the query structure). The<br />
optional name sets the name of this entry to a value other<br />
than the filename (the default). The name is displayed in<br />
the output file (see Examples, below). name cannot contain<br />
the file separator character (‘/’ on UNIX).<br />
DATABASE filename *scan* The absolute path to the database to scan with the query<br />
structure. The database can be generated in dbcreate<br />
mode. Default: database supplied with <strong>Prime</strong>.<br />
DBNAME filename *dbcreate* The name of the file in which to store the database create<br />
by ska. filename must be the file name without any path<br />
specification.<br />
FILELIST filename *dbcreate* A file containing a list of absolute filenames for structures<br />
(in PDB format) that are to be included in a database<br />
of templates that can be search with ska in scan<br />
mode. Absolute filenames are required to avoid having<br />
to copy large numbers of PDB files to the temporary<br />
directory in which the job is run.<br />
GAP_OPEN value *align*<br />
*scan*<br />
Gap initiation penalty.<br />
GAP_DEL value *align* Deletion penalty.
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