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At2g11090.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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/At2g11090-1wisA.pir.txt

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

Assigned types to 151 residues in Sequence 2-11090, 13 remain unknown
Assigned types to 86 residues in Sequence 1wisA, 78 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 44  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 45  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 46  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 47  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 68  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 69  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 70  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 71  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 102  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 103  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 104  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 105  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 106  All residues are positively and negatively charged

Translated sequence file At2g11090-1wisA.pir.txt into sequence alignment.

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

>1WIS.pdb  Made from 1830 ATOM records in 1WIS.pdb
GSSGSSGTISSGVPPELPGPPTNLGISNIGPRSVTLQFRPGYDGKTSISR
WLVEAQVGVVGEGEEWLLIHQLSNEPDARSMEVPDLNPFTCYSFRMRQVN
IVGTSPPSQPSRKIQTLQSGPSSG

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

Best alignment:
1WIS.pdb    70  HQLSNEPDAR    79
                HQ +  P  R
2-11090     16  HQQTTRPRGR    25

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

Highlighted IDENTICAL residue HIS   70  index1   70  path   16  %Seq  50.00
Highlighted IDENTICAL residue GLN   71  index1   71  path   17  %Seq  50.00
Highlighted IDENTICAL residue LEU   72  index1   72  path   18  %Seq  50.00
Highlighted IDENTICAL residue SER   73  index1   73  path   19  %Seq  50.00
Highlighted IDENTICAL residue ASN   74  index1   74  path   20  %Seq  50.00
Highlighted IDENTICAL residue GLU   75  index1   75  path   21  %Seq  50.00
Highlighted IDENTICAL residue PRO   76  index1   76  path   22  %Seq  50.00
Highlighted IDENTICAL residue ASP   77  index1   77  path   23  %Seq  50.00
Highlighted IDENTICAL residue ALA   78  index1   78  path   24  %Seq  50.00
Highlighted IDENTICAL residue ARG   79  index1   79  path   25  %Seq  50.00
Highlighted 10 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g11090-1wisA.pir.txt.1WIS.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g11090-1wisA.pir.txt PIR amino_acid 1WIS.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

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