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