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').
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/).