At2g06480.1/PDB

&&&&&&&&&&&&&&&&&&&& 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
Sequence 2
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g06480-2ore_D.pir.txt

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Assigned types to 52 residues in Sequence 2-06480, 1 remain unknown
Assigned types to 48 residues in Sequence 2ore_D, 5 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

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Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 29  All residues are positively and negatively charged

Translated sequence file At2g06480-2ore_D.pir.txt into sequence alignment.

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

>2ORE.pdb  Made from 5856 ATOM records in 2ORE.pdb
KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYIL
ADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQ
DPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFA
EKAQNAFFYCESYADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIA
EGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVDELLALYKPKNRAFLK
WAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDL
ISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAV
LFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAF
FYCESYADSMARADDASVVYCDPPYAPLSFTLEQQAHLAEIAEGLVERHI
PVLISNHDTMLTREWYQRAKLHVVKVKVDELLALYKPKNRAFLKWAGGKY
PLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNI
VKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLN
RYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESY
ADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIAEGLVERHIPVLIS
NHDTMLTREWYQRAKLHVVKVVDELLALYKP

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

Best alignment:
2ORE.pdb   102  PFRRAV   107
                PFRR V
2-06480     43  PFRRVV    48

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

Highlighted IDENTICAL residue PHE  105  index1  103  path   45  %Seq 100.00
Highlighted IDENTICAL residue ARG  107  index1  105  path   47  %Seq 100.00
Highlighted 2 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g06480-2ore_D.pir.txt.2ORE.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g06480-2ore_D.pir.txt PIR amino_acid 2ORE.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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