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_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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