Difference between revisions of "Lab Journal - Task 4 (PAH)"
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==Explore structural alignments== |
==Explore structural alignments== |
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==Evaluate sequence alignments== |
==Evaluate sequence alignments== |
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| + | The perl script hhmakemodel can be found in ''/usr/share/hhsuite/scripts''. It needs a input file in form of a result file from hhsearch with hit list and alignments (-i). |
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| + | |||
| + | -d <pdbdirs> directories containing the pdb files (for PDB, SCOP, or DALI |
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| + | sequences) (default=/cluster/databases/pdb/all) |
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| + | -m <int> [<int> ...] pick hits with specified indices (default='-m 1') |
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| + | -ts <file.pdb> write the PDB-formatted models based on *pairwise* |
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| + | alignments into file.pdb |
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Revision as of 10:49, 1 June 2013
Explore structural alignments
Evaluate sequence alignments
The perl script hhmakemodel can be found in /usr/share/hhsuite/scripts. It needs a input file in form of a result file from hhsearch with hit list and alignments (-i).
-d <pdbdirs> directories containing the pdb files (for PDB, SCOP, or DALI
sequences) (default=/cluster/databases/pdb/all)
-m <int> [<int> ...] pick hits with specified indices (default='-m 1')
-ts <file.pdb> write the PDB-formatted models based on *pairwise*
alignments into file.pdb
