At2g10940.1/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/At2g10940-1hyp_.pir.txt
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Assigned types to 291 residues in Sequence 2-10940, 1 remain unknown
Assigned types to 73 residues in Sequence 1hyp_, 219 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 At2g10940-1hyp_.pir.txt into sequence alignment.
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>1HYP.pdb Made from 656 ATOM records in 1HYP.pdb
PSCPDLSICLNILGGSLGTVDDCCALIGGLGDIEAIVCLCIQLRALGILN
LNRNLQLILNSCGRSYPSNATCPRT
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Best alignment:
1HYP.pdb 6 LSICLNILGG----SLG--TVDDCCALIGGLGDIEAIVCLC--IQLRALG 47
 L C+++LGG LG V+ CC L+ GL ++EA CLC ++L+AL 
2-10940 215 LGACVDLLGGLVKIGLGDPAVNKCCPLLKGLVEVEAAACLCTTLKLKALD 264
1HYP.pdb 48 I-LNLNRNLQLILNSCGRSYPSNATC 72
 + L + LQL+L +CG++ P TC
2-10940 265 LNLYVPVALQLLL-TCGKNPPPGYTC 289
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Highlighted IDENTICAL residue LEU 11 index1 6 path 215 %Seq 100.00
Highlighted IDENTICAL residue CYS 14 index1 9 path 218 %Seq 100.00
Highlighted IDENTICAL residue LEU 18 index1 13 path 222 %Seq 100.00
Highlighted IDENTICAL residue GLY 19 index1 14 path 223 %Seq 100.00
Highlighted IDENTICAL residue GLY 20 index1 15 path 224 %Seq 100.00
Highlighted IDENTICAL residue SER 21 index1 16 path 229 %Seq 50.00
Highlighted IDENTICAL residue LEU 22 index1 17 path 230 %Seq 50.00
Highlighted IDENTICAL residue GLY 23 index1 18 path 231 %Seq 50.00
Highlighted IDENTICAL residue VAL 25 index1 20 path 235 %Seq 100.00
Highlighted IDENTICAL residue CYS 28 index1 23 path 238 %Seq 100.00
Highlighted IDENTICAL residue CYS 29 index1 24 path 239 %Seq 100.00
Highlighted IDENTICAL residue LEU 31 index1 26 path 241 %Seq 100.00
Highlighted IDENTICAL residue GLY 34 index1 29 path 244 %Seq 100.00
Highlighted IDENTICAL residue LEU 35 index1 30 path 245 %Seq 100.00
Highlighted IDENTICAL residue GLU 39 index1 34 path 249 %Seq 100.00
Highlighted IDENTICAL residue ALA 40 index1 35 path 250 %Seq 100.00
Highlighted IDENTICAL residue CYS 43 index1 38 path 253 %Seq 100.00
Highlighted IDENTICAL residue LEU 44 index1 39 path 254 %Seq 100.00
Highlighted IDENTICAL residue CYS 45 index1 40 path 255 %Seq 100.00
Highlighted IDENTICAL residue ILE 46 index1 41 path 258 %Seq 100.00
Highlighted IDENTICAL residue GLY 52 index1 47 path 264 %Seq 50.00
Highlighted IDENTICAL residue ILE 53 index1 48 path 265 %Seq 50.00
Highlighted IDENTICAL residue LEU 54 index1 49 path 267 %Seq 100.00
Highlighted IDENTICAL residue LEU 60 index1 55 path 273 %Seq 100.00
Highlighted IDENTICAL residue GLN 61 index1 56 path 274 %Seq 100.00
Highlighted IDENTICAL residue LEU 62 index1 57 path 275 %Seq 100.00
Highlighted IDENTICAL residue LEU 64 index1 59 path 277 %Seq 100.00
Highlighted IDENTICAL residue CYS 67 index1 62 path 280 %Seq 100.00
Highlighted IDENTICAL residue GLY 68 index1 63 path 281 %Seq 100.00
Highlighted IDENTICAL residue PRO 72 index1 67 path 285 %Seq 100.00
Highlighted IDENTICAL residue THR 76 index1 71 path 289 %Seq 100.00
Highlighted IDENTICAL residue CYS 77 index1 72 path 290 %Seq 100.00
Highlighted 32 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10940-1hyp_.pir.txt.1HYP.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10940-1hyp_.pir.txt PIR amino_acid 1HYP.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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