At2g04240.1/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 Got here 4 Got here 3 Got here 4 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04240-1x4j_A.pir.txt

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Assigned types to 162 residues in Sequence 2-4240, 0 remain unknown Assigned types to 74 residues in Sequence 1x4j_A, 88 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 At2g04240-1x4j_A.pir.txt into sequence alignment.

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>1X4J.pdb Made from 1120 ATOM records in 1X4J.pdb GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHA KCVDKWLKANRTCPICRADSGPSSG

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Best alignment: 1X4J.pdb   26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA-NRTCPICR    67 C VC+ F+    +  L C H FH  C++KW+   N TCP+CR 2-4240    103  CSVCLSKFQGDSEINKLKCGHLFHKTCLEKWIDYWNITCPLCR   145

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Highlighted IDENTICAL residue CYS  26  index1   26  path  103  %Seq 100.00 Highlighted IDENTICAL residue VAL  28  index1   28  path  105  %Seq 100.00 Highlighted IDENTICAL residue CYS  29  index1   29  path  106  %Seq 100.00 Highlighted IDENTICAL residue PHE  33  index1   33  path  110  %Seq 100.00 Highlighted IDENTICAL residue LEU  42  index1   42  path  119  %Seq 100.00 Highlighted IDENTICAL residue CYS  44  index1   44  path  121  %Seq 100.00 Highlighted IDENTICAL residue HIS  46  index1   46  path  123  %Seq 100.00 Highlighted IDENTICAL residue PHE  48  index1   48  path  125  %Seq 100.00 Highlighted IDENTICAL residue HIS  49  index1   49  path  126  %Seq 100.00 Highlighted IDENTICAL residue CYS  52  index1   52  path  129  %Seq 100.00 Highlighted IDENTICAL residue LYS  55  index1   55  path  132  %Seq 100.00 Highlighted IDENTICAL residue TRP  56  index1   56  path  133  %Seq 100.00 Highlighted IDENTICAL residue ALA  59  index1   59  path  136  %Seq  50.00 Highlighted IDENTICAL residue ASN  60  index1   60  path  138  %Seq 100.00 Highlighted IDENTICAL residue THR  62  index1   62  path  140  %Seq 100.00 Highlighted IDENTICAL residue CYS  63  index1   63  path  141  %Seq 100.00 Highlighted IDENTICAL residue PRO  64  index1   64  path  142  %Seq 100.00 Highlighted IDENTICAL residue CYS  66  index1   66  path  144  %Seq 100.00 Highlighted IDENTICAL residue ARG  67  index1   67  path  145  %Seq 100.00 Highlighted 19 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04240-1x4j_A.pir.txt.1X4J.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04240-1x4j_A.pir.txt PIR amino_acid 1X4J.pdb A 100.0 BLOSUM62.dat

completed successfully.

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