Prime User Manual - ISP

106
Chapter 11: Command Syntax
Note that the actual 3D coordinates of the superposed structures are not written out by default
You must use ALISTRUCS_OUTFILE to write out the structures.
The following input file (align.inp):
QUERY_FILE query.pdb
TEMPLATE template.pdb
ALISTRUCS_OUTFILE superposition.pdb
saves the 3D coordinates of the aligned structures in the file superposition.pdb.
The following is a sample input file for database creation in dbcreate mode:
MODE dbcreate
FILELIST filelist.dat
DBNAME mydatabase.dat
The file filelist.dat contains the file names for the templates, including the path, as
follows:
/scr/templates/template-1.pdb
/scr/templates/template-2.pdb
/scr/templates/template-3.pdb
/scr/templates/template-4.pdb
A minimal input file for a scan is as follows:
MODE scan
QUERY_FILE query.pdb
Running ska with this input file would scan the database supplied with Prime for structural
analogs. The output from the structural search contains pairwise alignments between the query
structure and every structure in the database (assuming the two structures are sufficiently
similar). The results can be analyzed in a more convenient way with the graphical SKA Results
Viewer utility, $SCHRODINGER/utilities/SkaResultsViewer.
The use of the optional name argument is illustrated next. For the following input file:
QUERY_FILE query.pdb 1ctf
TEMPLATE 1dd3_A.pdb
the output file is as follows:
.........+.........+.........+.........+.........+.........+.....
1ctf 1 ceeeeeecc
1dd3_A 1 cchhhhhhhhhhhchhhhhhhhhhhhhhhcccchhhhhhhhhhhhhhhhhhhhhhccceeeeeecc
1ctf 1 ---------------------------------------------------------EFDVILKAA
1dd3_A 1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSF
Prime 2.1 User Manual