&&&&&&&&&&&&&&&&&&&& 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
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Got here 3
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Got here 3
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Got here 3
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Got here 3
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Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
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Got here 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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