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/At2g01870_1irjA.pir.txt

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

Assigned types to 157 residues in Sequence 2-01870, 5 remain unknown
Assigned types to 80 residues in Sequence 1irjA, 82 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 37  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 38  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 39  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 40  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 41  All residues are positively and negatively charged

Translated sequence file At2g01870_1irjA.pir.txt into sequence alignment.

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

>1IRJ.pdb  Made from 5587 ATOM records in 1IRJ.pdb
TCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK
ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLCKMSQLERNIETIIN
TFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLD
TNADKQLSFEEFIMLMARLKMSQLERNIETIINTFHQYSVKLGHPDTLNQ
GEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMA
RLMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKE
NKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLKMSQLERNIETIINTF
HQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTN
ADKQLSFEEFIMLMARLCKMSQLERNIETIINTFHQYSVKLGHPDTLNQG
EFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMAR
LCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK
ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTCKMSQLERNIETII
NTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDL
DTNADKQLSFEEFIMLMARL

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

Best alignment:
1IRJ.pdb    31  LNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEE    77
                +++ + +E +++  Q    + ++  ++I     D+    +  + FEE
2-01870     42  IDRDKAREALKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEE    88

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

Highlighted IDENTICAL residue GLU   39  index1   38  path   54  %Seq 100.00
Highlighted IDENTICAL residue GLN   46  index1   45  path   61  %Seq 100.00
Highlighted IDENTICAL residue ILE   59  index1   58  path   74  %Seq 100.00
Highlighted IDENTICAL residue ASP   65  index1   64  path   80  %Seq 100.00
Highlighted IDENTICAL residue PHE   76  index1   75  path   91  %Seq 100.00
Highlighted IDENTICAL residue GLU   77  index1   76  path   92  %Seq 100.00
Highlighted IDENTICAL residue GLU   78  index1   77  path   93  %Seq 100.00
Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01870_1irjA.pir.txt.1IRJ.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01870_1irjA.pir.txt PIR amino_acid 1IRJ.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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