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Difference between revisions of "buildModel.pl"
From MMTSB
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>TARGET | >TARGET | ||
| − | RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP >1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form | + | RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP |
| + | >1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form | ||
NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL.. | NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL.. | ||
Revision as of 14:45, 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.
Options
- -help
- usage information