At2g03390.1/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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03390-1vbvA0.pir.txt
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Assigned types to 330 residues in Sequence 2-03390, 0 remain unknown
Assigned types to 77 residues in Sequence 1vbvA0, 253 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 At2g03390-1vbvA0.pir.txt into sequence alignment.
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>1VBV.pdb Made from 603 ATOM records in 1VBV.pdb
ASKFGIGQQVRHSLLGYLGVVVDIDPVAAPWYHVVMEDDNGLPVHTYLAE
AQLSSELQDEHPEQPSMDELAQTIRKQ
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Best alignment:
1VBV.pdb 4 FGIGQQVRHSLLGYLGVVVDIDPVAA 29
 F +GQ++RH GY VV +DP+ +
2-03390 206 FRLGQKLRHKTFGYRAVVCGMDPICS 231
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Highlighted IDENTICAL residue PHE 6 index1 4 path 206 %Seq 100.00
Highlighted IDENTICAL residue GLY 9 index1 7 path 209 %Seq 100.00
Highlighted IDENTICAL residue GLN 10 index1 8 path 210 %Seq 100.00
Highlighted IDENTICAL residue ARG 13 index1 11 path 213 %Seq 100.00
Highlighted IDENTICAL residue HIS 14 index1 12 path 214 %Seq 100.00
Highlighted IDENTICAL residue GLY 18 index1 16 path 218 %Seq 100.00
Highlighted IDENTICAL residue TYR 19 index1 17 path 219 %Seq 100.00
Highlighted IDENTICAL residue VAL 22 index1 20 path 222 %Seq 100.00
Highlighted IDENTICAL residue VAL 23 index1 21 path 223 %Seq 100.00
Highlighted IDENTICAL residue ASP 27 index1 25 path 227 %Seq 100.00
Highlighted IDENTICAL residue PRO 28 index1 26 path 228 %Seq 100.00
Highlighted IDENTICAL residue ALA 49 index1 29 path 231 %Seq 50.00
Highlighted 12 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03390-1vbvA0.pir.txt.1VBV.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03390-1vbvA0.pir.txt PIR amino_acid 1VBV.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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