Preparing input files

The sample input files in this tutorial can be found in the examples/tutorial-model directory of the MODELLER distribution.

There are three kinds of input files: Protein Data Bank atom files with coordinates for the template structures, the alignment file with the alignment of the template structures with the target sequence, and MODELLER commands in a script file that instruct MODELLER what to do.

Atom files

Each atom file is named code.atm where code is a short protein code, preferably the PDB code; for example, Peptococcus aerogenes ferredoxin would be in a file 1fdx.atm. If you wish, you can also use file extensions .pdb and .ent instead of .atm. The code must be used as that protein's identifier throughout the modeling. The atom sets do not have to be superposed by the user before comparative modeling is done.

Alignment file

One of the formats for the alignment file is related to the PIR database format; this is the preferred format for comparative modeling:

C; A sample alignment in the PIR format; used in tutorial

>P1;5fd1
structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

>P1;1fdx
sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
-------------------------------*

See Section 2.4.1 for a detailed description of the alignment file format. Influence of the alignment on the quality of the model cannot be overemphasized. To obtain the best possible model, it is important to understand how the alignment is used by MODELLER[Šali & Blundell, 1993]. In outline, for the aligned regions, MODELLER tries to derive a 3D model for the target sequence that is as close to one or the other of the template structures as possible while also satisfying stereochemical restraints (e.g., bond lengths, angles, non-bonded atom contacts, ...); the inserted regions, which do not have any equivalent segments in any of the templates, are modeled in the context of the whole molecule, but using their sequence alone. This way of deriving a model means that whenever a user aligns a target residue with a template residue, he tells MODELLER to treat the aligned residues as structurally equivalent. Command CHECK_ALIGNMENT can be used to find some trivial alignment mistakes.

Script file

The script file contains commands for MODELLER, in the TOP language (Chapter 4). A sample script file model-default.top to produce one model of sequence 1fdx from the known structure of 5fd1 and from the alignment between the two sequences is

# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
SET ALNFILE  = 'alignment.ali'      # alignment filename
SET KNOWNS   = '5fd1'               # codes of the templates
SET SEQUENCE = '1fdx'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model 
SET ENDING_MODEL  = 1               # index of the last model
                                    # (determines how many models to calculate)
CALL ROUTINE = 'model'              # do homology modelling

See Section 3.2 for information about the model script and its arguments.