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
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Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
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Got here 3
Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02950-1c3gA.pir.txt

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

Assigned types to 439 residues in Sequence 2-02950, 2 remain unknown
Assigned types to 97 residues in Sequence 1c3gA, 344 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 At2g02950-1c3gA.pir.txt into sequence alignment.

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

>1C3G.pdb  Made from 1346 ATOM records in 1C3G.pdb
ETVQVNLPVSLEDLFVGKKKSFKIGRKGPHGASEKTQIDIQLKPGWKAGT
KITYKNQGDYNPQTGRRKTLQFVIQEKSHPNFKRDGDDLIYTLPLSFKES
LLGFSKTIQTIDGRTLPLSRVQPVQPSQTSTYPGQGMPTPKNPSQRGNLI
VKYKVDYPISLNDAQKRAID

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

Best alignment:
1C3G.pdb    18  KKKSFKIGRKGPHGASEKTQ    37
                K KSF+  R+  + +   TQ
2-02950    413  KPKSFETRRRISNSSISHTQ   432

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

Highlighted IDENTICAL residue LYS  197  index1   18  path  415  %Seq  50.00
Highlighted IDENTICAL residue LYS  198  index1   19  path  416  %Seq  50.00
Highlighted IDENTICAL residue LYS  199  index1   20  path  417  %Seq  50.00
Highlighted IDENTICAL residue SER  200  index1   21  path  418  %Seq  50.00
Highlighted IDENTICAL residue PHE  201  index1   22  path  419  %Seq  50.00
Highlighted IDENTICAL residue LYS  202  index1   23  path  420  %Seq  50.00
Highlighted IDENTICAL residue ILE  203  index1   24  path  421  %Seq  50.00
Highlighted IDENTICAL residue GLY  204  index1   25  path  422  %Seq  50.00
Highlighted IDENTICAL residue ARG  205  index1   26  path  423  %Seq  50.00
Highlighted IDENTICAL residue LYS  206  index1   27  path  424  %Seq  50.00
Highlighted IDENTICAL residue GLY  207  index1   28  path  425  %Seq  50.00
Highlighted IDENTICAL residue PRO  208  index1   29  path  426  %Seq  50.00
Highlighted IDENTICAL residue HIS  209  index1   30  path  427  %Seq  50.00
Highlighted IDENTICAL residue GLY  210  index1   31  path  428  %Seq  50.00
Highlighted IDENTICAL residue ALA  211  index1   32  path  429  %Seq  50.00
Highlighted IDENTICAL residue SER  212  index1   33  path  430  %Seq  50.00
Highlighted IDENTICAL residue GLU  213  index1   34  path  431  %Seq  50.00
Highlighted IDENTICAL residue LYS  214  index1   35  path  432  %Seq  50.00
Highlighted IDENTICAL residue THR  215  index1   36  path  433  %Seq  50.00
Highlighted IDENTICAL residue GLN  216  index1   37  path  434  %Seq  50.00
Highlighted 20 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02950-1c3gA.pir.txt.1C3G.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02950-1c3gA.pir.txt PIR amino_acid 1C3G.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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