DEPENDENCIES

• depends on lapack, and assumes the lapack is installed in /usr/lib/ (sudo apt install liblapack-dev)
• zlib (sudo apt install zlib)

INSTALLING

after unpacking in $STRUCT_HOME directory

> cd $STRUCT_HOME/10_objects/
> make
> make clean

the executable called struct should now be in $STRUCT_HOME

USAGE

$STRUCT_HOME/struct -in/-from <pdb/db tgt file> [-c1 <tgt chain>] \
		    [ -to <pdb/db qry file>] [ -c2 <qry chain>] \
		    [-max_out <number of almts to output>] [ -v] \
		    [-no_bb] [ -p <parameter file>]


  -from/to  input files in db or pdb format (to do the alignment 
          on backbone level, both files should be pdb
  -c1/2   chains for the pdb inputs 1 and 2
  -max_out number of alignments (pdb and allignemnt files) to output
  -no_bb  do not do the alignment on the backbone level
  -v      verbose output
  -p      parameter file

TEST CASES

1-on-1 comparison

> cd $STRUCT_HOME/11_tests/01_2d8bA_1d0nA/
> $STRUCT_HOME/struct -from 2d8bA.pdb  -to 1d0nA.pdb

view the results:

> cat   2d8bA_1d0nA.struct_out
> pymol 1d0nA.pdb 2d8bA.to_1d0nA.*.pdb

If you do not use pymol, you can view these files in your favorite molecular viewer by finding them under open->file menu.

Making a db file

A db file is a file containing directions and center points for each tentative, heuristically determined, element of secondary structure; it is used for fast searching though a large set of structures, such as PDB itself.

> cd $STRUCT_HOME/11_tests/01_2d8bA_1d0nA/
> $STRUCT_HOME/struct -in  1d0nA.pdb

Note: it is possible to use the full pdb file here, provided you have it available in your directory:

> $STRUCT_HOME/struct -in 1d0n.pdb -c1 A 

view the output:

> cat 1d0nA.db

Database search

> cd $STRUCT_HOME/11_tests/02_db_search
> $STRUCT_HOME/struct -from small_test.db -to ../01_2d8bA_1d0nA/2d8bA.db

View the output:

> cat digest.struct_out

View the output sorted by the direction score

> awk '$1 != "%" && $1 != "done"' digest.struct_out | sort -grk 5

Note: the "database" we are searching here is a
concatenation of the db files, like the one produced in
the testcase (b); direction is the only info we have in this case.