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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 == | ||
| − | == | + | <mmtsbToolExample cmd="buildModel.pl" set="test1"></mmtsbToolExample> |
Latest revision as of 14:54, 30 July 2009
Usage
usage: buildModel.pl [options] [fastaFile]
options: [-models value]
[-maxloop value]
[-verbose]
[-nocenter]
[-stats file]
[-pdbdir name]
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 ...