At2g02060.1/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 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 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/At2g02060-1zdfA.pir.txt

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Assigned types to 626 residues in Sequence 2-02060, 28 remain unknown Assigned types to 260 residues in Sequence 1zdfA, 394 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 At2g02060-1zdfA.pir.txt into sequence alignment.

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>1ZDF.pdb Made from 2049 ATOM records in 1ZDF.pdb MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKA LEIVFDEVITVDILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVF MDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLL HVASEQGSFDGGSQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPA FKAFGANAKVVHFLGQTKPWNYTYDTKTKSVRSMTHPQFLNVWWDIFTTS VVPLLQQF

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Best alignment: 1ZDF.pdb  153  ASEQGSFDGGSQGLLNTFFNSWATTDIRKHLP   184 SE G +D +  L     N   TT +  H P 2-02060    152  TSESGGYDDDADFLHIKKMND-TTTFLSHHFP   182

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Highlighted IDENTICAL residue ALA 152  index1  153  path  152  %Seq  50.00 Highlighted IDENTICAL residue SER 153  index1  154  path  153  %Seq  50.00 Highlighted IDENTICAL residue GLU 154  index1  155  path  154  %Seq  50.00 Highlighted IDENTICAL residue GLN 155  index1  156  path  155  %Seq  50.00 Highlighted IDENTICAL residue GLY 156  index1  157  path  156  %Seq  50.00 Highlighted IDENTICAL residue SER 157  index1  158  path  157  %Seq  50.00 Highlighted IDENTICAL residue PHE 158  index1  159  path  158  %Seq  50.00 Highlighted IDENTICAL residue ASP 159  index1  160  path  159  %Seq  50.00 Highlighted IDENTICAL residue GLY 160  index1  161  path  160  %Seq  50.00 Highlighted IDENTICAL residue GLY 161  index1  162  path  161  %Seq  50.00 Highlighted IDENTICAL residue SER 162  index1  163  path  162  %Seq  50.00 Highlighted IDENTICAL residue GLN 163  index1  164  path  163  %Seq  50.00 Highlighted IDENTICAL residue GLY 164  index1  165  path  164  %Seq  50.00 Highlighted IDENTICAL residue LEU 165  index1  166  path  165  %Seq  50.00 Highlighted IDENTICAL residue LEU 166  index1  167  path  166  %Seq  50.00 Highlighted IDENTICAL residue ASN 167  index1  168  path  167  %Seq  50.00 Highlighted IDENTICAL residue THR 168  index1  169  path  168  %Seq  50.00 Highlighted IDENTICAL residue PHE 169  index1  170  path  169  %Seq  50.00 Highlighted IDENTICAL residue PHE 170  index1  171  path  170  %Seq  50.00 Highlighted IDENTICAL residue ASN 171  index1  172  path  171  %Seq  50.00 Highlighted IDENTICAL residue SER 172  index1  173  path  172  %Seq  50.00 Highlighted IDENTICAL residue ALA 174  index1  175  path  173  %Seq  50.00 Highlighted IDENTICAL residue THR 175  index1  176  path  174  %Seq  50.00 Highlighted IDENTICAL residue THR 176  index1  177  path  175  %Seq  50.00 Highlighted IDENTICAL residue ASP 177  index1  178  path  176  %Seq  50.00 Highlighted IDENTICAL residue ILE 178  index1  179  path  177  %Seq  50.00 Highlighted IDENTICAL residue ARG 179  index1  180  path  178  %Seq  50.00 Highlighted IDENTICAL residue LYS 180  index1  181  path  179  %Seq  50.00 Highlighted IDENTICAL residue HIS 181  index1  182  path  180  %Seq  50.00 Highlighted IDENTICAL residue LEU 182  index1  183  path  181  %Seq  50.00 Highlighted IDENTICAL residue PRO 183  index1  184  path  182  %Seq  50.00 Highlighted 31 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02060-1zdfA.pir.txt.1ZDF.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02060-1zdfA.pir.txt PIR amino_acid 1ZDF.pdb A 100.0 BLOSUM62.dat

completed successfully.

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