T.I.T.O. keywords

MANDATORY
ALIMSF Input filename of the alignment in MSF (GCG) format (see the various alignment file formats below)

STTMDL Output filenames (.pdb, .log, .top, .ali to be associated to the root name)

STTSPT PDB input filename

POLCHA Label of the protein chain within the polypeptide chain to be read from the PDB input

SEQSPT Sequence name corresponding to the PDB input

SEQMDL Sequence names. More than one SEQMDL may be listed. The sequences are used to check the sequence-structure compatibility. However, the only modelled protein is that of the first sequence

GRAFIK   1 A written report

OPTIONAL
MODLER   2   Create two files to run MODELLER 4.0 with secondary structure constraints

or MODLER   1   Create two files to run MODELLER 4.0 without constraints

or MODLER   0   Without running MODELLER

FRANCE   1   Comments are written in french ; for comments in english set to   FRANCE   0

First example of an input file:
  • xva.inp
    List of alignment file formats accepted by TITO:
    MSF multi-sequence format used by GCG 8.0/9.0 software (Keyword ALIMSF in the input filename of the alignment)

    MUL for a MSF file from Multalin (Keyword ALIMUL in the input filename of the alignment)

    MAT for a MSF file from MatchBoxin (Keyword ALIMAT in the input filename of the alignment)

    PIR for a PIR file format (Keyword ALIPIR in the input filename of the alignment)

    MAS for an alignment edited by the program SEAVIEW (Keyword ALIMAS in the input filename of the alignment)

    FAS for a FASTA file format (Keyword ALIFAS in the input filename of the alignment)

    CLU for an alignment from ClustalW (Keyword ALICLU in the input filename of the alignment)

    List of alignment files from web servers and programs accepted by TITO:
    3DPSSM (Keyword ALI3DP in the input filename of the alignment)

    PSI-BLAST (Keyword ALIPSI in the input filename of the alignment)

    mGenThreader (Keyword ALIMGT in the input filename of the alignment)

    HMMer (Keyword ALIHMM in the input filename of the alignment)

    INBGU (Keyword ALIGBU in the input filename of the alignment)

    NPSA (Keyword ALINPS in the input filename of the alignment)

    MPSA (Keyword ALIMPS in the input filename of the alignment)