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Difference between revisions of "buildModel.pl"
From MMTSB
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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 | ||
| + | RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ | ||
| + | KTDAASKPFAEVRILSCGELIP | ||
| + | >1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form | ||
| + | NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENV | ||
| + | EVK-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> | ||
== Options == | == Options == | ||
Revision as of 14:44, 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 RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ
KTDAASKPFAEVRILSCGELIP
>1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENV
EVK-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.
Options
- -help
- usage information