Model building

Once a target-template alignment is constructed, MODELLER calculates a 3D model of the target completely automaticaly. The following script will generate five similar models of TvLDH based on the 4mdhA template structure and the alignment in file `TvLDH-4mdh.ali' (file `model-single.top').

1.81.0

INCLUDE
SET ALNFILE = 'TvLDH-4mdh.ali'
SET KNOWNS = '4mdhA'
SET SEQUENCE = 'TvLDH'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
CALL ROUTINE = 'model'

The first line includes many standard variable and routine definitions. The following five lines set parameter values for the `model' routine. ALNFILE  names the file that contains the target-template alignment in the PIR format. KNOWNS  defines the known template structure(s) in ALNFILE  (`TvLDH-4mdh.ali'). SEQUENCE  defines the name of the target sequence in ALNFILE . STARTING_MODEL  and ENDING_MODEL  define the number of models that are calculated (their indices will run from 1 to 5). The last line in the file calls the `model' routine that actually calculates the models. The most important output files are `model.log', which reports warnings, errors and other useful information including the input restraints used for modeling that remain violated in the final model; and `TvLDH.B99990001', which contains the model coordinates in the PDB format. The model can be viewed by any program that reads the PDB format, such as MODVIEW (http://guitar.rockefeller.edu/modview/).