At2g07090.1/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/

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

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
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
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/At2g07090-1ic2_A.pir.txt

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

Assigned types to 159 residues in Sequence 2-07090, 0 remain unknown
Assigned types to 63 residues in Sequence 1ic2_A, 96 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

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Translated sequence file At2g07090-1ic2_A.pir.txt into sequence alignment.

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>1IC2.pdb  Made from 2492 ATOM records in 1IC2.pdb
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKL
KGTEDELDKYSESLKDAQEKLELADKKATMDAIKKKMQMLKLDKENALDR
AEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKL
ELADKKMDAIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELV
ALQKKLKGTEDELDKYSESLKDAQEKLELADKKATMDAIKKKMQMLKLDK
ENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLK
DAQEKLELADKK

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

Best alignment:
1IC2.pdb    20  DRAEQAEADKKAAEERSKQLEDELVALQKKL    50
                +   + +A+      + ++L++E +A +K+L
2-07090     91  NEISKVKAETNEMLNQIQELKEEAIARKKEL   121

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

Highlighted IDENTICAL residue LEU   39  index1   39  path  110  %Seq 100.00
Highlighted IDENTICAL residue LYS   49  index1   49  path  120  %Seq 100.00
Highlighted IDENTICAL residue LEU   50  index1   50  path  121  %Seq 100.00
Highlighted 3 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g07090-1ic2_A.pir.txt.1IC2.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g07090-1ic2_A.pir.txt PIR amino_acid 1IC2.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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