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
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
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/At2g02590-1fx8A.pir.txt

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

Assigned types to 324 residues in Sequence 2-02590, 24 remain unknown
Assigned types to 184 residues in Sequence 1fx8A, 164 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 230  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 231  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 232  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 233  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 234  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 235  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 286  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 287  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 288  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 289  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 290  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 291  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 292  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 293  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 322  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 323  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 324  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 325  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 326  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 327  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 328  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 329  All residues are positively and negatively charged

Translated sequence file At2g02590-1fx8A.pir.txt into sequence alignment.

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

>1FX8.pdb  Made from 1895 ATOM records in 1FX8.pdb
TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMA
IYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVY
GLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVI
TAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPA
RDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLI
GRHL

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

Best alignment:
1FX8.pdb    34  FGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIP    83
                FG  + +V++ L     I L   +   +      + L  F+       +P
2-02590    143  FGWPDEAVVFALATLPVIELRGAIPVGYWMQLKPVVLTSFSVLGNMVPVP   192

1FX8.pdb    84  FIV    86
                FIV
2-02590    193  FIV   195

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

Highlighted IDENTICAL residue PHE   39  index1   34  path  143  %Seq 100.00
Highlighted IDENTICAL residue GLY   40  index1   35  path  144  %Seq 100.00
Highlighted IDENTICAL residue VAL   46  index1   41  path  150  %Seq 100.00
Highlighted IDENTICAL residue LEU   50  index1   45  path  154  %Seq 100.00
Highlighted IDENTICAL residue ILE   56  index1   51  path  160  %Seq 100.00
Highlighted IDENTICAL residue LEU   58  index1   53  path  162  %Seq 100.00
Highlighted IDENTICAL residue LEU   67  index1   62  path  171  %Seq  50.00
Highlighted IDENTICAL residue ASN   68  index1   63  path  172  %Seq  50.00
Highlighted IDENTICAL residue PRO   69  index1   64  path  173  %Seq  50.00
Highlighted IDENTICAL residue ALA   70  index1   65  path  174  %Seq 100.00
Highlighted IDENTICAL residue THR   72  index1   67  path  176  %Seq 100.00
Highlighted IDENTICAL residue ALA   74  index1   69  path  178  %Seq 100.00
Highlighted IDENTICAL residue LYS   85  index1   80  path  189  %Seq  50.00
Highlighted 13 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02590-1fx8A.pir.txt.1FX8.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02590-1fx8A.pir.txt PIR amino_acid 1FX8.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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