At2g04240.1/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/
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Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
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Sequence 1
Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04240-1x4j_A.pir.txt
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Assigned types to 162 residues in Sequence 2-4240, 0 remain unknown
Assigned types to 74 residues in Sequence 1x4j_A, 88 remain unknown
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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 At2g04240-1x4j_A.pir.txt into sequence alignment.
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>1X4J.pdb Made from 1120 ATOM records in 1X4J.pdb
GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHA
KCVDKWLKANRTCPICRADSGPSSG
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Best alignment:
1X4J.pdb 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA-NRTCPICR 67
 C VC+ F+ + L C H FH C++KW+ N TCP+CR
2-4240 103 CSVCLSKFQGDSEINKLKCGHLFHKTCLEKWIDYWNITCPLCR 145
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Highlighted IDENTICAL residue CYS 26 index1 26 path 103 %Seq 100.00
Highlighted IDENTICAL residue VAL 28 index1 28 path 105 %Seq 100.00
Highlighted IDENTICAL residue CYS 29 index1 29 path 106 %Seq 100.00
Highlighted IDENTICAL residue PHE 33 index1 33 path 110 %Seq 100.00
Highlighted IDENTICAL residue LEU 42 index1 42 path 119 %Seq 100.00
Highlighted IDENTICAL residue CYS 44 index1 44 path 121 %Seq 100.00
Highlighted IDENTICAL residue HIS 46 index1 46 path 123 %Seq 100.00
Highlighted IDENTICAL residue PHE 48 index1 48 path 125 %Seq 100.00
Highlighted IDENTICAL residue HIS 49 index1 49 path 126 %Seq 100.00
Highlighted IDENTICAL residue CYS 52 index1 52 path 129 %Seq 100.00
Highlighted IDENTICAL residue LYS 55 index1 55 path 132 %Seq 100.00
Highlighted IDENTICAL residue TRP 56 index1 56 path 133 %Seq 100.00
Highlighted IDENTICAL residue ALA 59 index1 59 path 136 %Seq 50.00
Highlighted IDENTICAL residue ASN 60 index1 60 path 138 %Seq 100.00
Highlighted IDENTICAL residue THR 62 index1 62 path 140 %Seq 100.00
Highlighted IDENTICAL residue CYS 63 index1 63 path 141 %Seq 100.00
Highlighted IDENTICAL residue PRO 64 index1 64 path 142 %Seq 100.00
Highlighted IDENTICAL residue CYS 66 index1 66 path 144 %Seq 100.00
Highlighted IDENTICAL residue ARG 67 index1 67 path 145 %Seq 100.00
Highlighted 19 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04240-1x4j_A.pir.txt.1X4J.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04240-1x4j_A.pir.txt PIR amino_acid 1X4J.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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