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At2g12695.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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/

======================================================

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

======================================================

Assigned types to 130 residues in Sequence 2-12695, 0 remain unknown
Assigned types to 62 residues in Sequence 1nknA, 68 remain unknown

======================================================

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

======================================================

Translated sequence file At2g12695-1nknA.pir.txt into sequence alignment.

======================================================

>1NKN.pdb  Made from 2495 ATOM records in 1NKN.pdb
MKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDKV
EELLSKNYHLENEVARLKKLVGEREEEMKEQLKQMDKMKEDLAKTERIKK
ELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGE
EMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDK
VEELLSKNYHLENEVARLKKLVGEREEEMKEQLKQMDKMKEDLAKTERIK
KELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVG
E

======================================================

Best alignment:
1NKN.pdb   137  LENEVARLKKLVGEEMKEQLKQMDKMKEDLA   167
                 ++E++  K  V  E++     + ++KE+LA
2-12695     80  FDSELSAAKSEVSVELEALQAMVKELKEELA   110

======================================================

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

===============================================================================

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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@


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