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At2g10940.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
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Sequence 2
Got here 3
Got here 4
Got here 3
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Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g10940-1hyp_.pir.txt

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

Assigned types to 291 residues in Sequence 2-10940, 1 remain unknown
Assigned types to 73 residues in Sequence 1hyp_, 219 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 At2g10940-1hyp_.pir.txt into sequence alignment.

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

>1HYP.pdb  Made from 656 ATOM records in 1HYP.pdb
PSCPDLSICLNILGGSLGTVDDCCALIGGLGDIEAIVCLCIQLRALGILN
LNRNLQLILNSCGRSYPSNATCPRT

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

Best alignment:
1HYP.pdb     6  LSICLNILGG----SLG--TVDDCCALIGGLGDIEAIVCLC--IQLRALG    47
                L  C+++LGG     LG   V+ CC L+ GL ++EA  CLC  ++L+AL 
2-10940    215  LGACVDLLGGLVKIGLGDPAVNKCCPLLKGLVEVEAAACLCTTLKLKALD   264

1HYP.pdb    48  I-LNLNRNLQLILNSCGRSYPSNATC    72
                + L +   LQL+L +CG++ P   TC
2-10940    265  LNLYVPVALQLLL-TCGKNPPPGYTC   289

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

Highlighted IDENTICAL residue LEU   11  index1    6  path  215  %Seq 100.00
Highlighted IDENTICAL residue CYS   14  index1    9  path  218  %Seq 100.00
Highlighted IDENTICAL residue LEU   18  index1   13  path  222  %Seq 100.00
Highlighted IDENTICAL residue GLY   19  index1   14  path  223  %Seq 100.00
Highlighted IDENTICAL residue GLY   20  index1   15  path  224  %Seq 100.00
Highlighted IDENTICAL residue SER   21  index1   16  path  229  %Seq  50.00
Highlighted IDENTICAL residue LEU   22  index1   17  path  230  %Seq  50.00
Highlighted IDENTICAL residue GLY   23  index1   18  path  231  %Seq  50.00
Highlighted IDENTICAL residue VAL   25  index1   20  path  235  %Seq 100.00
Highlighted IDENTICAL residue CYS   28  index1   23  path  238  %Seq 100.00
Highlighted IDENTICAL residue CYS   29  index1   24  path  239  %Seq 100.00
Highlighted IDENTICAL residue LEU   31  index1   26  path  241  %Seq 100.00
Highlighted IDENTICAL residue GLY   34  index1   29  path  244  %Seq 100.00
Highlighted IDENTICAL residue LEU   35  index1   30  path  245  %Seq 100.00
Highlighted IDENTICAL residue GLU   39  index1   34  path  249  %Seq 100.00
Highlighted IDENTICAL residue ALA   40  index1   35  path  250  %Seq 100.00
Highlighted IDENTICAL residue CYS   43  index1   38  path  253  %Seq 100.00
Highlighted IDENTICAL residue LEU   44  index1   39  path  254  %Seq 100.00
Highlighted IDENTICAL residue CYS   45  index1   40  path  255  %Seq 100.00
Highlighted IDENTICAL residue ILE   46  index1   41  path  258  %Seq 100.00
Highlighted IDENTICAL residue GLY   52  index1   47  path  264  %Seq  50.00
Highlighted IDENTICAL residue ILE   53  index1   48  path  265  %Seq  50.00
Highlighted IDENTICAL residue LEU   54  index1   49  path  267  %Seq 100.00
Highlighted IDENTICAL residue LEU   60  index1   55  path  273  %Seq 100.00
Highlighted IDENTICAL residue GLN   61  index1   56  path  274  %Seq 100.00
Highlighted IDENTICAL residue LEU   62  index1   57  path  275  %Seq 100.00
Highlighted IDENTICAL residue LEU   64  index1   59  path  277  %Seq 100.00
Highlighted IDENTICAL residue CYS   67  index1   62  path  280  %Seq 100.00
Highlighted IDENTICAL residue GLY   68  index1   63  path  281  %Seq 100.00
Highlighted IDENTICAL residue PRO   72  index1   67  path  285  %Seq 100.00
Highlighted IDENTICAL residue THR   76  index1   71  path  289  %Seq 100.00
Highlighted IDENTICAL residue CYS   77  index1   72  path  290  %Seq 100.00
Highlighted 32 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10940-1hyp_.pir.txt.1HYP.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10940-1hyp_.pir.txt PIR amino_acid 1HYP.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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