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At2g01190.1/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

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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01190_2cu1_A.pir.txt

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

Assigned types to 720 residues in Sequence 2-01190, 2 remain unknown
Assigned types to 96 residues in Sequence 2cu1_A, 626 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

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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 98  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 99  All residues are positively and negatively charged

Translated sequence file At2g01190_2cu1_A.pir.txt into sequence alignment.

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

>2CU1.pdb  Made from 1612 ATOM records in 2CU1.pdb
GSSGSSGDVRVKFEHRGEKRILQFPRPVKLEDLRSKAKIAFGQSMDLHYT
NNELVIPLTTQDDLDKAVELLDRSIHMKSLKILLVINGSTQATNLEPSGP
SSG

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

Best alignment:
2CU1.pdb    17  GEKRILQFPRPVKLEDL--RSKAKIAFGQSMDLHY--TNNEL--VIPLTT    60
                G+ RI+   R   L  L  R    +  G+S  L Y   + +L  +I +TT
2-01190     99  GDTRIVVVDRNSSLPSLIARLSNTLLDGRSFTLKYQLPSEDLDSLISVTT   148

2CU1.pdb    61  QDDLDKAVELLDRSI    75
                 +DLD  +E  DR+I
2-01190    149  DEDLDNMIEEYDRTI   163

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

Highlighted IDENTICAL residue GLY   17  index1   17  path  101  %Seq 100.00
Highlighted IDENTICAL residue ARG   20  index1   20  path  104  %Seq 100.00
Highlighted IDENTICAL residue ILE   21  index1   21  path  105  %Seq 100.00
Highlighted IDENTICAL residue ARG   26  index1   26  path  110  %Seq 100.00
Highlighted IDENTICAL residue LEU   30  index1   30  path  114  %Seq 100.00
Highlighted IDENTICAL residue LEU   33  index1   33  path  117  %Seq 100.00
Highlighted IDENTICAL residue ALA   40  index1   40  path  126  %Seq  50.00
Highlighted IDENTICAL residue PHE   41  index1   41  path  127  %Seq  50.00
Highlighted IDENTICAL residue GLY   42  index1   42  path  128  %Seq 100.00
Highlighted IDENTICAL residue SER   44  index1   44  path  130  %Seq 100.00
Highlighted IDENTICAL residue LEU   47  index1   47  path  133  %Seq 100.00
Highlighted IDENTICAL residue TYR   49  index1   49  path  135  %Seq 100.00
Highlighted IDENTICAL residue THR   50  index1   50  path  138  %Seq  50.00
Highlighted IDENTICAL residue LEU   54  index1   54  path  142  %Seq 100.00
Highlighted IDENTICAL residue ILE   56  index1   56  path  146  %Seq 100.00
Highlighted IDENTICAL residue THR   59  index1   59  path  149  %Seq 100.00
Highlighted IDENTICAL residue THR   60  index1   60  path  150  %Seq 100.00
Highlighted IDENTICAL residue ASP   63  index1   63  path  153  %Seq 100.00
Highlighted IDENTICAL residue LEU   64  index1   64  path  154  %Seq 100.00
Highlighted IDENTICAL residue ASP   65  index1   65  path  155  %Seq 100.00
Highlighted IDENTICAL residue GLU   69  index1   69  path  159  %Seq 100.00
Highlighted IDENTICAL residue ASP   72  index1   72  path  162  %Seq 100.00
Highlighted IDENTICAL residue ARG   73  index1   73  path  163  %Seq 100.00
Highlighted IDENTICAL residue SER   74  index1   74  path  164  %Seq  50.00
Highlighted IDENTICAL residue ILE   75  index1   75  path  165  %Seq  50.00
Highlighted 25 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01190_2cu1_A.pir.txt.2CU1.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01190_2cu1_A.pir.txt PIR amino_acid 2CU1.pdb A 100.0 BLOSUM62.dat 

completed successfully.

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

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