At2g13550.1/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
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/At2g13550-1bfp_.pir.txt
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Assigned types to 181 residues in Sequence 2-13550, 8 remain unknown
Assigned types to 158 residues in Sequence 1bfp_, 31 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 46 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 47 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 59 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 60 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
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 102 All residues are positively and negatively charged
Translated sequence file At2g13550-1bfp_.pir.txt into sequence alignment.
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>1BFP.pdb Made from 1765 ATOM records in 1BFP.pdb
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT
GKLPVPWPTLVTTFVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDD
GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYIM
ADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLST
QSALSKDPNEKRDHMVLLEFVTAAGI
======================================================
Best alignment:
1BFP.pdb 173 VQLADHYQQNTPIGDGPVLLPDNHY 197
 + L +Q NT G P P++H+
2-13550 13 MHLPTQFQPNTRTGRQPKSPPNSHH 37
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Highlighted IDENTICAL residue LEU 178 index1 175 path 15 %Seq 100.00
Highlighted IDENTICAL residue ASP 180 index1 177 path 17 %Seq 100.00
Highlighted IDENTICAL residue TYR 182 index1 179 path 19 %Seq 100.00
Highlighted IDENTICAL residue GLN 183 index1 180 path 20 %Seq 50.00
Highlighted IDENTICAL residue GLY 189 index1 186 path 26 %Seq 50.00
Highlighted IDENTICAL residue ASP 190 index1 187 path 27 %Seq 100.00
Highlighted IDENTICAL residue PRO 192 index1 189 path 29 %Seq 100.00
Highlighted 7 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13550-1bfp_.pir.txt.1BFP.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13550-1bfp_.pir.txt PIR amino_acid 1BFP.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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