FANDOM


&&&&&&&&&&&&&&&&&&&& 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/

======================================================

Sequence file type = 3

Sequence type = 3

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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03140-1a8s_.pir.txt

======================================================

Assigned types to 1805 residues in Sequence 2-03140, 8 remain unknown
Assigned types to 271 residues in Sequence 1a8s_, 1542 remain unknown

======================================================

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

======================================================

Translated sequence file At2g03140-1a8s_.pir.txt into sequence alignment.

======================================================

>1A8S.pdb  Made from 2085 ATOM records in 1A8S.pdb
TTFTTRDGTQIYYKDWGSGQPIVFSHGWPLNADSWESQMIFLAAQGYRVI
AHDRRGHGRSSQPWSGNDMDTYADDLAQLIEHLDLRDAVLFGFSTGGGEV
ARYIGRHGTARVAKAGLISAVPPLMLKTEANPGGLPMEVFDGIRQASLAD
RSQLYKDLASGPFFGFNQPGAKSSAGMVDWFWLQGMAAGHKNAYDCIKAF
SETDFTEDLKKIDVPTLVVHGDADQVVPIEASGIASAALVKGSTLKIYSG
APHGLTDTHKDQLNADLLAFIKG

======================================================

Best alignment:
1A8S.pdb   116  GLISAVPPLMLKTEANPGGLPME   138
                GL+S     +  ++ +PGG+ +E
2-03140    697  GLVSGSDETISGSDNSPGGVELE   719

======================================================

Highlighted IDENTICAL residue GLY  116  index1  116  path  705  %Seq  50.00
Highlighted IDENTICAL residue LEU  117  index1  117  path  706  %Seq  50.00
Highlighted IDENTICAL residue ILE  118  index1  118  path  707  %Seq  50.00
Highlighted IDENTICAL residue SER  119  index1  119  path  708  %Seq  50.00
Highlighted IDENTICAL residue ALA  120  index1  120  path  709  %Seq  50.00
Highlighted IDENTICAL residue VAL  121  index1  121  path  710  %Seq  50.00
Highlighted IDENTICAL residue PRO  122  index1  122  path  711  %Seq  50.00
Highlighted IDENTICAL residue PRO  123  index1  123  path  712  %Seq  50.00
Highlighted IDENTICAL residue LEU  124  index1  124  path  713  %Seq  50.00
Highlighted IDENTICAL residue MET  125  index1  125  path  714  %Seq  50.00
Highlighted IDENTICAL residue LEU  126  index1  126  path  715  %Seq  50.00
Highlighted IDENTICAL residue LYS  127  index1  127  path  716  %Seq  50.00
Highlighted IDENTICAL residue THR  128  index1  128  path  717  %Seq  50.00
Highlighted IDENTICAL residue GLU  129  index1  129  path  718  %Seq  50.00
Highlighted IDENTICAL residue ALA  130  index1  130  path  719  %Seq  50.00
Highlighted IDENTICAL residue ASN  131  index1  131  path  720  %Seq  50.00
Highlighted IDENTICAL residue PRO  132  index1  132  path  721  %Seq  50.00
Highlighted IDENTICAL residue GLY  133  index1  133  path  722  %Seq  50.00
Highlighted IDENTICAL residue GLY  134  index1  134  path  723  %Seq  50.00
Highlighted IDENTICAL residue LEU  135  index1  135  path  724  %Seq  50.00
Highlighted IDENTICAL residue PRO  136  index1  136  path  725  %Seq  50.00
Highlighted IDENTICAL residue MET  137  index1  137  path  726  %Seq  50.00
Highlighted IDENTICAL residue GLU  138  index1  138  path  727  %Seq  50.00
Highlighted 23 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03140-1a8s_.pir.txt.1A8S.pdb.conservation.pml

===============================================================================

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03140-1a8s_.pir.txt PIR amino_acid 1A8S.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

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