At2g06555.1/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
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Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g06555-2haqt_C.pir.txt
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Assigned types to 159 residues in Sequence 2-06555, 9 remain unknown
Assigned types to 125 residues in Sequence 2aqt_C, 43 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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Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 52 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 53 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 54 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 55 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 56 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 100 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 101 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 136 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 137 All residues are positively and negatively charged
Translated sequence file At2g06555-2haqt_C.pir.txt into sequence alignment.
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>2AQT.pdb Made from 3456 ATOM records in 2AQT.pdb
ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIH
ENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTV
LHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMA
CGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLH
GFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDL
PALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGG
GPRMACGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGL
SEGLHGFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDA
HLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPA
PLGGGGPRMACGVIK
======================================================
Best alignment:
2AQT.pdb 128 IHTGGDNHSDHPAPLGGGGPRMACGVIKASIEV 160
 + + +SD G CGV+ V
2-06555 126 VFVSENEYSDFLLEASDVGKERRCGVLMLECRV 158
======================================================
Highlighted IDENTICAL residue SER 167 index1 136 path 143 %Seq 100.00
Highlighted IDENTICAL residue ASP 168 index1 137 path 144 %Seq 100.00
Highlighted IDENTICAL residue GLY 177 index1 146 path 153 %Seq 100.00
Highlighted IDENTICAL residue CYS 182 index1 151 path 158 %Seq 100.00
Highlighted IDENTICAL residue GLY 183 index1 152 path 159 %Seq 100.00
Highlighted IDENTICAL residue VAL 184 index1 153 path 160 %Seq 100.00
Highlighted IDENTICAL residue LYS 186 index1 155 path 162 %Seq 50.00
Highlighted IDENTICAL residue ALA 32 index1 156 path 163 %Seq 50.00
Highlighted IDENTICAL residue SER 33 index1 157 path 164 %Seq 50.00
Highlighted IDENTICAL residue ILE 34 index1 158 path 165 %Seq 50.00
Highlighted IDENTICAL residue GLU 35 index1 159 path 166 %Seq 50.00
Highlighted IDENTICAL residue VAL 36 index1 160 path 167 %Seq 50.00
Highlighted 12 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g06555-2haqt_C.pir.txt.2AQT.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g06555-2haqt_C.pir.txt PIR amino_acid 2AQT.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@