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/At2g14880-1v31A.pir.txt

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

Assigned types to 141 residues in Sequence 2-14880-141, 0 remain unknown
Assigned types to 83 residues in Sequence 1v31A, 58 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 At2g14880-1v31A.pir.txt into sequence alignment.

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

>1V31.pdb  Made from 1426 ATOM records in 1V31.pdb
GSSGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPND
PSFFNCDAALQKVFGEEKLKFTMVSQKISHHLSPPPPSGPSSG

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

Best alignment:
1V31.pdb        7  GVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNC    56
                   G+ +   +S  + D++ +    R + +  IW Y+K   LQ+P +     C
2-14880-141    64  GIMKPRPVSPEMQDIVELPEIARTQALKRIWAYIKEHDLQDPQNKREILC   113

1V31.pdb       57  DAALQKVF-GEEKLKFTMVSQKISHH    81
                   D  L+K+F G +++ F  +++ I  H
2-14880-141   114  DEKLKKIFEGRDRVGFLEIAKLIGPH   139

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

Highlighted IDENTICAL residue GLY    7  index1    7  path   64  %Seq 100.00
Highlighted IDENTICAL residue SER   15  index1   15  path   72  %Seq 100.00
Highlighted IDENTICAL residue ASP   20  index1   20  path   77  %Seq 100.00
Highlighted IDENTICAL residue ARG   29  index1   29  path   86  %Seq 100.00
Highlighted IDENTICAL residue ILE   36  index1   36  path   93  %Seq 100.00
Highlighted IDENTICAL residue TRP   37  index1   37  path   94  %Seq 100.00
Highlighted IDENTICAL residue TYR   39  index1   39  path   96  %Seq 100.00
Highlighted IDENTICAL residue LYS   41  index1   41  path   98  %Seq 100.00
Highlighted IDENTICAL residue LEU   45  index1   45  path  102  %Seq 100.00
Highlighted IDENTICAL residue GLN   46  index1   46  path  103  %Seq 100.00
Highlighted IDENTICAL residue PRO   48  index1   48  path  105  %Seq 100.00
Highlighted IDENTICAL residue CYS   56  index1   56  path  113  %Seq 100.00
Highlighted IDENTICAL residue ASP   57  index1   57  path  114  %Seq 100.00
Highlighted IDENTICAL residue LEU   60  index1   60  path  117  %Seq 100.00
Highlighted IDENTICAL residue LYS   62  index1   62  path  119  %Seq 100.00
Highlighted IDENTICAL residue PHE   64  index1   64  path  121  %Seq 100.00
Highlighted IDENTICAL residue GLY   65  index1   65  path  123  %Seq 100.00
Highlighted IDENTICAL residue PHE   71  index1   71  path  129  %Seq 100.00
Highlighted IDENTICAL residue ILE   78  index1   78  path  136  %Seq 100.00
Highlighted IDENTICAL residue HIS   81  index1   81  path  139  %Seq 100.00
Highlighted 20 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14880-1v31A.pir.txt.1V31.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14880-1v31A.pir.txt PIR amino_acid 1V31.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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