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
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
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13150-2fxm_A.pir.txt

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

Assigned types to 262 residues in Sequence 2-13150, 0 remain unknown
Assigned types to 123 residues in Sequence 2fxm_A, 139 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 At2g13150-2fxm_A.pir.txt into sequence alignment.

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

>2FXM.pdb  Made from 1953 ATOM records in 2FXM.pdb
PLLKSAEREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDL
QLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMNAELT
AKKRKLEDECSELKRDIDDLELTLAKASMKEEFTRLKEALEKSEARRKEL
EEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMN
ERLEDEEEMNAELTAKKRKLEDECSELKRDIDDLELTL

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

Best alignment:
2FXM.pdb     3  LKSAEREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQL    52
                +  + + KE+AS  +E  R+   L+  E+  +  ++K+  ++    +L+L
2-13150    137  IAKSTKLKEVASDPKEVRRI---LKNQESAARSKQKKLQYMI----NLEL   179

2FXM.pdb    53  QVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMNAEL-TA   101
                ++   ++  A   E+   L  +K     + KE+  R+E  E+ +AEL  A
2-13150    180  KINFLENKNASIFEKIKLLENDKTMRMNEKKEIMIRIESLEQ-HAELRDA   228

2FXM.pdb   102  KKRKLEDECSELK   114
                    L  E   LK
2-13150    229  LTEHLHVEIERLK   241

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

Highlighted IDENTICAL residue LEU  840  index1    3  path  137  %Seq  50.00
Highlighted IDENTICAL residue LYS  847  index1   10  path  144  %Seq 100.00
Highlighted IDENTICAL residue GLU  848  index1   11  path  145  %Seq 100.00
Highlighted IDENTICAL residue ALA  850  index1   13  path  147  %Seq 100.00
Highlighted IDENTICAL residue SER  851  index1   14  path  148  %Seq 100.00
Highlighted IDENTICAL residue GLU  855  index1   18  path  152  %Seq 100.00
Highlighted IDENTICAL residue ARG  858  index1   21  path  155  %Seq 100.00
Highlighted IDENTICAL residue GLU  867  index1   30  path  161  %Seq 100.00
Highlighted IDENTICAL residue LEU  880  index1   43  path  174  %Seq 100.00
Highlighted IDENTICAL residue LEU  887  index1   50  path  177  %Seq 100.00
Highlighted IDENTICAL residue GLN  892  index1   55  path  182  %Seq 100.00
Highlighted IDENTICAL residue GLU  894  index1   57  path  184  %Seq 100.00
Highlighted IDENTICAL residue ILE  909  index1   72  path  199  %Seq 100.00
Highlighted IDENTICAL residue VAL  919  index1   82  path  209  %Seq 100.00
Highlighted IDENTICAL residue GLU  935  index1   98  path  224  %Seq 100.00
Highlighted IDENTICAL residue LEU  943  index1  106  path  233  %Seq 100.00
Highlighted IDENTICAL residue LEU  950  index1  113  path  240  %Seq 100.00
Highlighted 17 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13150-2fxm_A.pir.txt.2FXM.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13150-2fxm_A.pir.txt PIR amino_acid 2FXM.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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