At2g12695.1/PDB

&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&
Successfully read 2 file paths from WYRM_file_paths.txt
generic_input /usr/local/www/html/proteins/workspace/
generic_output /usr/local/www/html/proteins/htdocs/results/
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Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g12695-1nknA.pir.txt
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Assigned types to 130 residues in Sequence 2-12695, 0 remain unknown
Assigned types to 62 residues in Sequence 1nknA, 68 remain unknown
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Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
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Translated sequence file At2g12695-1nknA.pir.txt into sequence alignment.
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>1NKN.pdb Made from 2495 ATOM records in 1NKN.pdb
MKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDKV
EELLSKNYHLENEVARLKKLVGEREEEMKEQLKQMDKMKEDLAKTERIKK
ELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGE
EMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDK
VEELLSKNYHLENEVARLKKLVGEREEEMKEQLKQMDKMKEDLAKTERIK
KELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVG
E
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Best alignment:
1NKN.pdb 137 LENEVARLKKLVGEEMKEQLKQMDKMKEDLA 167
 ++E++ K V E++ + ++KE+LA
2-12695 80 FDSELSAAKSEVSVELEALQAMVKELKEELA 110
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Highlighted IDENTICAL residue GLU 908 index1 140 path 83 %Seq 100.00
Highlighted IDENTICAL residue VAL 909 index1 141 path 84 %Seq 100.00
Highlighted IDENTICAL residue GLN 849 index1 155 path 98 %Seq 100.00
Highlighted IDENTICAL residue ASP 854 index1 160 path 103 %Seq 100.00
Highlighted IDENTICAL residue MET 856 index1 162 path 105 %Seq 100.00
Highlighted 5 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g12695-1nknA.pir.txt.1NKN.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g12695-1nknA.pir.txt PIR amino_acid 1NKN.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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