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/At2g13550-1bfp_.pir.txt

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

Assigned types to 181 residues in Sequence 2-13550, 8 remain unknown
Assigned types to 158 residues in Sequence 1bfp_, 31 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

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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 46  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 47  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 59  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 60  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 99  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 100  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 101  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 102  All residues are positively and negatively charged

Translated sequence file At2g13550-1bfp_.pir.txt into sequence alignment.

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

>1BFP.pdb  Made from 1765 ATOM records in 1BFP.pdb
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT
GKLPVPWPTLVTTFVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDD
GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYIM
ADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLST
QSALSKDPNEKRDHMVLLEFVTAAGI

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

Best alignment:
1BFP.pdb   173  VQLADHYQQNTPIGDGPVLLPDNHY   197
                + L   +Q NT  G  P   P++H+
2-13550     13  MHLPTQFQPNTRTGRQPKSPPNSHH    37

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

Highlighted IDENTICAL residue LEU  178  index1  175  path   15  %Seq 100.00
Highlighted IDENTICAL residue ASP  180  index1  177  path   17  %Seq 100.00
Highlighted IDENTICAL residue TYR  182  index1  179  path   19  %Seq 100.00
Highlighted IDENTICAL residue GLN  183  index1  180  path   20  %Seq  50.00
Highlighted IDENTICAL residue GLY  189  index1  186  path   26  %Seq  50.00
Highlighted IDENTICAL residue ASP  190  index1  187  path   27  %Seq 100.00
Highlighted IDENTICAL residue PRO  192  index1  189  path   29  %Seq 100.00
Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13550-1bfp_.pir.txt.1BFP.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13550-1bfp_.pir.txt PIR amino_acid 1BFP.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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