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 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 Got here 4 Got here 3 Got here 4 Got here 3 Sequence 2 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 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  LSICLNILGGSLG--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

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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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