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

Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
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Got here 3
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Got here 3
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Got here 3
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Got here 3
Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02060-1zdfA.pir.txt

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

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

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

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

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

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

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

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

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

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.

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

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