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
Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02970-1u6zA.pir.txt

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

Assigned types to 555 residues in Sequence 2-02970, 8 remain unknown
Assigned types to 313 residues in Sequence 1u6zA, 250 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 At2g02970-1u6zA.pir.txt into sequence alignment.

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

>1U6Z.pdb  Made from 8205 ATOM records in 1U6Z.pdb
EFAAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLGPDNMLSEEA
MTRGLNCLSLFAERLQGFSPASVCIVGTHTLRQALNATDFLKRAEKVIPY
PIEIISGNEEARLIFMGVEHTQPEKGRKLVIDIGGGSTELVIGENFEPIL
VESRRMGCVSFAQLYFPGGVINKENFQRARMAAAQKLETLTWQFRIQGWN
VAMGASGTIKAAHEVLMEMGEKDGIITPERLEKLVKEVLRHRNFASLSLP
GLSEERKTVFVPGLAILCGVFDALAIRELRLSDGALREGVLYEMEGRFRH
QDVRSRTASSLANQYHIDSEQARRVLDTTMQMYEQWREQQPKLAHPQLEA
LLRWAAMLHEVGLNINHSGLHRHSAYILQNSDLPGFNQEQQLMMATLVRY
HRKAIKLDDLPRFTLFKKKQFLPLIQLLRLGVLLNNQRQATTTPPTLTLI
TDDSHWTLRFPHDWFSQNALVLLDLEKEQEYWEGVAGWRLKIEEESTPEF
AAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLGPDNMLSEEAMT
RGLNCLSLFAERLQGFSPASVCIVGTHTLRQALNATDFLKRAEKVIPYPI
EIISGNEEARLIFMGVEHTQPEKGRKLVIDIGGGSTELVIGENFEPILVE
SRRMGCVSFAQLYFPGGVINKENFQRARMAAAQKLETLTWQFRIQGWNVA
MGASGTIKAAHEVLMEMGEKDGIITPERLEKLVKEVLRHRNFASLSLPGL
SEERKTVFVPGLAILCGVFDALAIRELRLSDGALREGVLYEMEGRFRHQD
VRSRTASSLANQYHIDSEQARRVLDTTMQMYEQWREQQPKLAHPQLEALL
RWAAMLHEVGLNINHSGLHRHSAYILQNSDLPGFNQEQQLMMATLVRYHR
KAIKLDDLPRFTLFKKKQFLPLIQLLRLGVLLNNQRQATTTPPTLTLITD
DSHWTLRFPHDWFSQNALVLLDLEKEQEYWEGVAGWRLKIEEESTPEI

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

Best alignment:
1U6Z.pdb   239  LRHRNFASLSL-PGLS   253
                 R  N+ASL L PGLS
2-02970    116  FRGANYASLKLHPGLS   131

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

Highlighted IDENTICAL residue HIS  252  index1  241  path  118  %Seq 100.00
Highlighted IDENTICAL residue LEU  260  index1  249  path  126  %Seq 100.00
Highlighted IDENTICAL residue GLY  262  index1  251  path  129  %Seq 100.00
Highlighted IDENTICAL residue LEU  263  index1  252  path  130  %Seq 100.00
Highlighted 4 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02970-1u6zA.pir.txt.1U6Z.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02970-1u6zA.pir.txt PIR amino_acid 1U6Z.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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