&&&&&&&&&&&&&&&&&&&& 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_1fi6A.pir.txt
======================================================
Assigned types to 157 residues in Sequence 2-01870, 3 remain unknown
Assigned types to 88 residues in Sequence 1fi6A, 72 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 55 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 56 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 57 All residues are positively and negatively charged
Translated sequence file At2g01870_1fi6A.pir.txt into sequence alignment.
======================================================
>1FI6.pdb Made from 1496 ATOM records in 1FI6.pdb
WKITDEQRQYYVNQFKTIQPDLNGFIPGSAAKEFFTKSKLPILELSHIWE
LSDFDKDGALTLDEFCAAFHLVVARKNGYDLPEKLPESLMPK
======================================================
Best alignment:
1FI6.pdb 71 LVVARKNGYDLPEKLPE 87
+ K D PE +PE
2-01870 115 FITVIKPSMDGPESVPE 131
======================================================
Highlighted IDENTICAL residue LEU 76 index1 71 path 118 %Seq 50.00
Highlighted IDENTICAL residue VAL 77 index1 72 path 119 %Seq 50.00
Highlighted IDENTICAL residue VAL 78 index1 73 path 120 %Seq 50.00
Highlighted IDENTICAL residue ALA 79 index1 74 path 121 %Seq 50.00
Highlighted IDENTICAL residue ARG 80 index1 75 path 122 %Seq 50.00
Highlighted IDENTICAL residue LYS 81 index1 76 path 123 %Seq 50.00
Highlighted IDENTICAL residue ASN 82 index1 77 path 124 %Seq 100.00
Highlighted IDENTICAL residue PRO 91 index1 86 path 133 %Seq 100.00
Highlighted 8 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01870_1fi6A.pir.txt.1FI6.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01870_1fi6A.pir.txt PIR amino_acid 1FI6.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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