Preparing input files for MPACK
alignment obtained from Fold-recognition servers (http://www.bioinfo.pl/meta, http://www.genesilico.pl/ or http://bioserv.cbs.cnrs.fr/HTML_BIO/frame_meta.html
) or hand edited
alignments should be formatted in an appropriate format
(CLUSTALW format). One can ALIGNREP to achieve this from a crude alignment.
ALIGNREP reformats the alignment into appropriate format which has to renamed
with an extension *.aln. Before proceeding modeling
with MPACK, make sure that you have complete target amino acid residues.
Alignment file (s)
sure that there is no special characters, like space coma or non
alphanumeric character in the template/target.
- Gaps should
be indicated by "-" and not by "."
case of disulfide bond in the template, replace CYS (C) residue in the target by small letter
20 capital alphabets and one small alphabet for Cys, c
selenomethionine will be indicated by "X". Edit this to "M" and
edit the template pdb file accordingly.
in sequence alignment there are unknown residues are marked with "X".
One should edit it back to the original residue if any in PDB file.
- If one
wants to use multiple templates or small fragments then appropriate
alignments containing those regions should be given as an alignment
(starting number of the target residue contained in these files should
be mentioned separately). All alignment files
must follow the alignment rules.
PDB files can be obtained from RCSB (http://www.rcsb.org). Almost in all cases to have consistency while modeling
it is recommended to spend time to look into the header files of the PDB.
In some cases it may be required to edit the file.
carefully the SS Bonds information from PDB
file. If you have any matching CYS residues in the template and the target,
then most probably the target may also have similar SS bonds.
sure that the amino acid residues in the target PDB file and the alignment
must match exactly, otherwise it will crash the program before run.
PDB file should end with TER followed by
END and the PDB file must have extension