INSTALLATION
Pcons5 Installation notes


1) To unpack the tarball:

kantarell$ tar -xvzf pcons5.tar.gz

this will put everything the folder "pcons5_dir/"


2) Two environmental variables, PROQDIR and PCONS5DIR, needs to be set
in order for the program to run.

In bash shell this is done my the following commands:
export PROQDIR=/home/bjornw/bin/pcons5_dir/
export PCONS5DIR=/home/bjornw/bin/pcons5_dir/

where "/home/bjornw/bin/pcons5_dir/" should be the path to where the
program is installed.


3) RUNNING

3.1) THE INPUT FILE

Pcons5 takes a list of protein models as input exemplified by
"infile.small" below, each line contains the full path to a protein
model:

kantarell$ head infile.small
testdir/1fl9A.1ak2.foldfit.10.bb
testdir/1fl9A.1ake_A.foldfit.8.bb
testdir/1fl9A.1b0u_A.foldfit.2.bb
testdir/1fl9A.1b0u_A.mgenthreader.4.bb
testdir/1fl9A.1cc0_A.inbgu.10.bb
testdir/1fl9A.1d2n_A.orfeus.6.bb
testdir/1fl9A.1d6j_A.orfeus.10.bb
testdir/1fl9A.1e32_A.mgenthreader.9.bb
testdir/1fl9A.1e32_A.orfeus.5.bb
testdir/1fl9A.1ega_A.foldfit.7.bb

3.2) THE PDB FILE

To simplify the running all information needed should be in the PDB
file one example is showed below:

kantarell$ head testdir/1fl9A.1ak2.foldfit.10.bb
REMARK SS CCCEEEEEEEEECCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCEEEEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCHHHHHCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHHHC
REMARK METHOD foldfit
MODEL 10
PARENT 1AK2
REMARK DATE     1996-06-11
REMARK SCORE    2.01e+01        0.90
REMARK The numbering of the residue changed to match the
REMARK correct structure: Fri Apr 11 15:42:35 2003./BW
SEQRES   1    127  GLU LYS ALA ILE MET VAL TYR LEU ASN GLY ASP LEU GLY 
SEQRES   2    127  ALA GLY LYS THR THR LEU THR ARG GLY MET LEU GLN GLY 
.
.
.


Description
----------
The information used by Pcons are the following lines (the others are optional)

REMARK SS - is the predicted secondary structure for the model
REMARK SCORE - is the method score (e.g. 2.01e+01)
MODEL - is the rank from that method (e.g. 10)
REMARK METHOD - is the specific method (e.g. foldfit) 

4) EXCUTING

If everything is set up correctly, Pcons5 runs using the input file
descriped above.

There are two testfiles that can be used to check that everything is
set up OK.  infile.small (takes a few minutes to run) and infile.large
(takes 30 min to run). The output from these files are in
infile.small.out and infile.large.out.

Example:
kantarell$ ./pcons5 infile.small
testdir/1fl9A.1ak2.foldfit.10.bb                  0.9898  0.9898  1.0167  0.0884  0.6574  0.0471  0.0000
testdir/1fl9A.1ake_A.foldfit.8.bb                 1.0632  1.1549  1.1353  0.0392  0.6444  0.0984  0.0000
testdir/1fl9A.1b0u_A.foldfit.2.bb                 1.5379  1.3084  1.6753  0.0470  0.6146  1.0000  0.0000
testdir/1fl9A.1b0u_A.mgenthreader.4.bb            1.0781  1.1312  0.8933 -0.0119  0.2830  0.7360  0.0000
testdir/1fl9A.1cc0_A.inbgu.10.bb                  0.8581  1.1457  1.0345  0.0040  0.1696  0.0000  0.0000
testdir/1fl9A.1d2n_A.orfeus.6.bb                  1.1890  1.1933  1.2650 -0.0320  0.0542  0.9782  0.0000
testdir/1fl9A.1d6j_A.orfeus.10.bb                 1.1367  1.1031  1.2290  0.0102  0.0668  0.8910  0.0000
testdir/1fl9A.1e32_A.mgenthreader.9.bb            1.1421  1.2218  1.2931  0.0152  0.4709  0.3280  0.0000
testdir/1fl9A.1e32_A.orfeus.5.bb                  1.2664  1.1990  1.4146  0.0020  0.1303  0.9864  0.0000
testdir/1fl9A.1ega_A.foldfit.7.bb                 0.7144  0.7144  0.6885  0.1427  0.6325  0.1064  0.0000


1st column  - model
2nd column  - Pcons5 score
3rd column  - consensus all
4th column  - consensus first
5th column  - ProQMX
6th column  - ProQLG
7th column  - Score "good"
8th column  - Score "very good"


Hope everything work, do not hesitate to email me if something does
not work or look strange.

/Björn
bjorn@sbc.su.se