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/At2g03850-2b9cA.pir.txt

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

Assigned types to 191 residues in Sequence 2-03850, 0 remain unknown
Assigned types to 141 residues in Sequence 2b9cB, 50 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 At2g03850-2b9cA.pir.txt into sequence alignment.

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

>2B9C.pdb  Made from 2301 ATOM records in 2B9C.pdb
ELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQ
LKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEL
KTVTNNLKSLEDKVEELLSKNYHLENEVARLKKLVGQLVEEELDRAQERL
ATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAE
DADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKS
LEDKVEELLSKNYHLENEVARLKKLVGE

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

Best alignment:
2B9C.pdb   108  KSLEDKVEELLSKNYHLENEVARLKKLVGQLVEEELDRAQ----ERLATA   153
                K L+D  ++         +EV       GQ V + +DRA+    E+ + A
2-03850     67  KWLDDASQKASDYVKEKGSEVGHASAQKGQDVNDHVDRAKYYMFEKASEA   116

2B9C.pdb   154  LQKLEE-AEKAAD-ESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAED   201
                +  + E A+ A++  +E+G +  +  A   E+  +    +  E   IA D
2-03850    117  IDNVAEIAQFASEFVTEKGKETKKETASISEKAKDFIVEKAGEIIDIATD   166

2B9C.pdb   202  ADRK   205
                  +K
2-03850    167  VSKK   170

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

Highlighted IDENTICAL residue ASP  209  index1  112  path   71  %Seq 100.00
Highlighted IDENTICAL residue VAL  211  index1  114  path   73  %Seq 100.00
Highlighted IDENTICAL residue GLU 1098  index1  142  path  101  %Seq  50.00
Highlighted IDENTICAL residue ARG 1105  index1  149  path  112  %Seq 100.00
Highlighted IDENTICAL residue THR 1108  index1  152  path  115  %Seq 100.00
Highlighted IDENTICAL residue GLU 1115  index1  159  path  122  %Seq  50.00
Highlighted IDENTICAL residue ASP 1121  index1  165  path  129  %Seq 100.00
Highlighted IDENTICAL residue GLU 1124  index1  168  path  133  %Seq 100.00
Highlighted IDENTICAL residue ALA 1134  index1  178  path  143  %Seq 100.00
Highlighted IDENTICAL residue GLU 1138  index1  182  path  147  %Seq 100.00
Highlighted IDENTICAL residue MET 1141  index1  185  path  150  %Seq 100.00
Highlighted IDENTICAL residue GLU 1145  index1  189  path  154  %Seq  50.00
Highlighted IDENTICAL residue HIS 1153  index1  197  path  162  %Seq 100.00
Highlighted IDENTICAL residue LYS 1161  index1  205  path  170  %Seq 100.00
Highlighted 14 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03850-2b9cA.pir.txt.2B9C.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03850-2b9cA.pir.txt PIR amino_acid 2B9C.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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