MMTSB
Tool Set Documentation

Difference between revisions of "BuildModel.pl"

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== Description ==
 
== Description ==
  
 +
This script is used for template-based structure prediction. It takes an alignment file in FASTA file as input, finds the PDB template, builds
 +
a homology model and adds missing (loop) residues via Modeller.<BR>
 +
 +
A typical input file is expected to look as follows:<BR>
 +
 +
>TARGET
 +
RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP 
 +
>1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form
 +
NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL..
 +
 +
Note the PDB code and chain ID in the third line. A properly formatted file
 +
can be generated with the [[psiblast.pl]] tool from PSI-Blast output.<BR>
 +
 +
For this tool to work, it is necessary to have a local copy of the PDB (or
 +
at least a directory where the structures for the needed templates are
 +
present) either at the location pointed to by the environment variable <TT>PDBDIR</TT> or given through the option <TT>-pdbdir</TT>.<BR>
 +
 +
Furthermore, Modeller needs to be installed and available. The script will
 +
try to guess the location of the Modeller script that can be called with
 +
a Modeller input file, but it is better
 +
to provide the location through the environment variable <TT>MODELLEREXEC</TT>.<BR>
  
 
== Options ==
 
== Options ==
  
 
; -help : usage information
 
; -help : usage information
 
+
; -models value : number of models to generate (only the best model is returned)
 +
; -maxloop value : maximum loop size to model automatically
 +
; -verbose : extensive output about various steps of the modeling protocol
 +
; -nocenter : do not center resulting structure
 +
; -stats file : generate a file with information about the generated model(s)
 +
; -pdbdir name : directory where PDB database is located
  
 
== Examples ==
 
== Examples ==
 +
 +
<mmtsbToolExample cmd="buildModel.pl" set="test1"></mmtsbToolExample>

Latest revision as of 22:53, 13 September 2010

Usage

usage:   buildModel.pl [options] [fastaFile]
options:               [-models value]
                       [-maxloop value]
                       [-verbose]
                       [-nocenter]
                       [-stats file]
                       [-pdbdir name]
Show source


Description

This script is used for template-based structure prediction. It takes an alignment file in FASTA file as input, finds the PDB template, builds a homology model and adds missing (loop) residues via Modeller.

A typical input file is expected to look as follows:

>TARGET 
RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP   
>1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form
NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL..

Note the PDB code and chain ID in the third line. A properly formatted file can be generated with the psiblast.pl tool from PSI-Blast output.

For this tool to work, it is necessary to have a local copy of the PDB (or at least a directory where the structures for the needed templates are present) either at the location pointed to by the environment variable PDBDIR or given through the option -pdbdir.

Furthermore, Modeller needs to be installed and available. The script will try to guess the location of the Modeller script that can be called with a Modeller input file, but it is better to provide the location through the environment variable MODELLEREXEC.

Options

-help 
usage information
-models value 
number of models to generate (only the best model is returned)
-maxloop value 
maximum loop size to model automatically
-verbose 
extensive output about various steps of the modeling protocol
-nocenter 
do not center resulting structure
-stats file 
generate a file with information about the generated model(s)
-pdbdir name 
directory where PDB database is located

Examples

buildModel.pl -models 3 alignment
generate three template-based model according to the given alignment and return the best model

ATOM      1  N   ARG     1      -0.147  20.265  18.017  0.00  0.00      1SG 
ATOM      2  CA  ARG     1       0.690  19.995  17.181  0.00  0.00      1SG 
ATOM      3  CB  ARG     1       1.286  21.273  16.588  0.00  0.00      1SG 
ATOM      4  CG  ARG     1       0.360  22.003  15.629  0.00  0.00      1SG 
ATOM      5  CD  ARG     1      -0.938  22.404  16.312  0.00  0.00      1SG 
ATOM      6  NE  ARG     1      -1.797  21.251  16.574  0.00  0.00      1SG 
ATOM      7  CZ  ARG     1      -1.718  20.493  17.663  0.00  0.00      1SG 
ATOM      8  NH1 ARG     1      -0.817  20.765  18.597  0.00  0.00      1SG 
ATOM      9  NH2 ARG     1      -2.542  19.465  17.816  0.00  0.00      1SG 
ATOM     10  C   ARG     1       1.609  19.459  17.187  0.00  0.00      1SG 

...