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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04240-1x4j_A.pir.txt

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

Assigned types to 162 residues in Sequence 2-4240, 0 remain unknown
Assigned types to 74 residues in Sequence 1x4j_A, 88 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 At2g04240-1x4j_A.pir.txt into sequence alignment.

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

>1X4J.pdb  Made from 1120 ATOM records in 1X4J.pdb
GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHA
KCVDKWLKANRTCPICRADSGPSSG

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

Best alignment:
1X4J.pdb    26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA-NRTCPICR    67
                C VC+  F+    +  L C H FH  C++KW+   N TCP+CR
2-4240     103  CSVCLSKFQGDSEINKLKCGHLFHKTCLEKWIDYWNITCPLCR   145

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

Highlighted IDENTICAL residue CYS   26  index1   26  path  103  %Seq 100.00
Highlighted IDENTICAL residue VAL   28  index1   28  path  105  %Seq 100.00
Highlighted IDENTICAL residue CYS   29  index1   29  path  106  %Seq 100.00
Highlighted IDENTICAL residue PHE   33  index1   33  path  110  %Seq 100.00
Highlighted IDENTICAL residue LEU   42  index1   42  path  119  %Seq 100.00
Highlighted IDENTICAL residue CYS   44  index1   44  path  121  %Seq 100.00
Highlighted IDENTICAL residue HIS   46  index1   46  path  123  %Seq 100.00
Highlighted IDENTICAL residue PHE   48  index1   48  path  125  %Seq 100.00
Highlighted IDENTICAL residue HIS   49  index1   49  path  126  %Seq 100.00
Highlighted IDENTICAL residue CYS   52  index1   52  path  129  %Seq 100.00
Highlighted IDENTICAL residue LYS   55  index1   55  path  132  %Seq 100.00
Highlighted IDENTICAL residue TRP   56  index1   56  path  133  %Seq 100.00
Highlighted IDENTICAL residue ALA   59  index1   59  path  136  %Seq  50.00
Highlighted IDENTICAL residue ASN   60  index1   60  path  138  %Seq 100.00
Highlighted IDENTICAL residue THR   62  index1   62  path  140  %Seq 100.00
Highlighted IDENTICAL residue CYS   63  index1   63  path  141  %Seq 100.00
Highlighted IDENTICAL residue PRO   64  index1   64  path  142  %Seq 100.00
Highlighted IDENTICAL residue CYS   66  index1   66  path  144  %Seq 100.00
Highlighted IDENTICAL residue ARG   67  index1   67  path  145  %Seq 100.00
Highlighted 19 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04240-1x4j_A.pir.txt.1X4J.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04240-1x4j_A.pir.txt PIR amino_acid 1X4J.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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