&&&&&&&&&&&&&&&&&&&& 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
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
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13150-2fxm_A.pir.txt
======================================================
Assigned types to 262 residues in Sequence 2-13150, 0 remain unknown
Assigned types to 123 residues in Sequence 2fxm_A, 139 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 At2g13150-2fxm_A.pir.txt into sequence alignment.
======================================================
>2FXM.pdb Made from 1953 ATOM records in 2FXM.pdb
PLLKSAEREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDL
QLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMNAELT
AKKRKLEDECSELKRDIDDLELTLAKASMKEEFTRLKEALEKSEARRKEL
EEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMN
ERLEDEEEMNAELTAKKRKLEDECSELKRDIDDLELTL
======================================================
Best alignment:
2FXM.pdb 3 LKSAEREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQL 52
+ + + KE+AS +E R+ L+ E+ + ++K+ ++ +L+L
2-13150 137 IAKSTKLKEVASDPKEVRRI---LKNQESAARSKQKKLQYMI----NLEL 179
2FXM.pdb 53 QVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMNAEL-TA 101
++ ++ A E+ L +K + KE+ R+E E+ +AEL A
2-13150 180 KINFLENKNASIFEKIKLLENDKTMRMNEKKEIMIRIESLEQ-HAELRDA 228
2FXM.pdb 102 KKRKLEDECSELK 114
L E LK
2-13150 229 LTEHLHVEIERLK 241
======================================================
Highlighted IDENTICAL residue LEU 840 index1 3 path 137 %Seq 50.00
Highlighted IDENTICAL residue LYS 847 index1 10 path 144 %Seq 100.00
Highlighted IDENTICAL residue GLU 848 index1 11 path 145 %Seq 100.00
Highlighted IDENTICAL residue ALA 850 index1 13 path 147 %Seq 100.00
Highlighted IDENTICAL residue SER 851 index1 14 path 148 %Seq 100.00
Highlighted IDENTICAL residue GLU 855 index1 18 path 152 %Seq 100.00
Highlighted IDENTICAL residue ARG 858 index1 21 path 155 %Seq 100.00
Highlighted IDENTICAL residue GLU 867 index1 30 path 161 %Seq 100.00
Highlighted IDENTICAL residue LEU 880 index1 43 path 174 %Seq 100.00
Highlighted IDENTICAL residue LEU 887 index1 50 path 177 %Seq 100.00
Highlighted IDENTICAL residue GLN 892 index1 55 path 182 %Seq 100.00
Highlighted IDENTICAL residue GLU 894 index1 57 path 184 %Seq 100.00
Highlighted IDENTICAL residue ILE 909 index1 72 path 199 %Seq 100.00
Highlighted IDENTICAL residue VAL 919 index1 82 path 209 %Seq 100.00
Highlighted IDENTICAL residue GLU 935 index1 98 path 224 %Seq 100.00
Highlighted IDENTICAL residue LEU 943 index1 106 path 233 %Seq 100.00
Highlighted IDENTICAL residue LEU 950 index1 113 path 240 %Seq 100.00
Highlighted 17 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13150-2fxm_A.pir.txt.2FXM.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13150-2fxm_A.pir.txt PIR amino_acid 2FXM.pdb _ 100.0 BLOSUM62.dat
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@
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