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mk_map

readme.md

Convert GREMLIN/CCMPRED results to .map files

  • see "cmd" file for full example!
  • aln file: containing the alignment used as input to GREMLIN/CCMPRED (after gap removal).
  • cut file: One line containing the full sequence, the second line containing the trimmed sequence (with "-" to indicated positions removed). This file is used to determine the mapping from the matrix file to the full length sequence.
  • mtx file: symmetric matrix containing length x length values of coupling results.
  • chk file: (NOT required) for profile generation, binary file from csbuild. To generate this file you'll need the a3m/fas file before gap removal. This alignment is then given as input to csbuild. csbuild is used to add context-specific pseudocounts to the profiles.
    • csbuild -i TMP.a3m -I a3m -o TMP.chk -O chk -D csblast-2.2.3/data/K4000.crf
  • A perl script is provided to convert the data to a contact map file:
    • perl mk_map.pl -aln TMP.aln -cut TMP.cut -mtx TMP.mtx -chk TMP.chk -map TMP.map -do_apc
    • the "-do_apc" flag is REQUIRED if no APC (Average Product Correction) was performed to input mtx.

Convert PDB to .map files

  • see "cmd_pdb2map" file for full example!
  • pdb file: single chain, single model, no HETATM
  • chk file: (see above for more information)
    • WARNING: the PDB numbering should match the the input FASTA file
    • hhblits -o /dev/null -d DATABASE -cpu ??? -id 90 -cov 75 -e 1E-10 -n 2 -i TMP.fasta -oa3m TMP.a3m
    • csbuild -i TMP.a3m -I a3m -o TMP.chk -O chk -D csblast-2.2.3/data/K4000.crf
  • ss file: output from stride (secondary structure)
    • stride TMP.pdb > TMP.ss
    • WARNING: stride only reads ATOM records!
  • A perl script is provided to convert the data to a contact map file:
    • perl pdb2map.pl -pdb TMP.pdb -new_pdb TMP.fix.pdb -map TMP.map -chk TMP.chk -ss TMP.ss
    • -new_pdb outputs a new pdb renumbered to match the map numbering
    • -ss and -chk files are NOT required
    • WARNING: only single chain supported at this time!