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/At2g10550-c1pia_.pir.txt

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

Assigned types to 170 residues in Sequence 2-10550, 20 remain unknown
Assigned types to 169 residues in Sequence c1puia_, 21 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

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

Translated sequence file At2g10550-c1pia_.pir.txt into sequence alignment.

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

>1PUI.pdb  Made from 2613 ATOM records in 1PUI.pdb
FVMSAPDIRHLPSDTGIEVAFAGRSNAGKSSALNTLTNQQLINLFEVADG
KRLVDLPGYGEMKRKWQRALGEYLEKRQSLQGLVVLMDIRHPLKDLDQQM
IEWAVDSNIAVLVLLTKADKLASGARKAQLNMVREAVLAFNGDVQVETFS
SLKKQGVDKLRQKLDTWFSVMSAPDIRHLPSDTGIEVAFAGRSNAGKSSA
LNTLTNQLINLFEVADGKRLVDLPGYRKWQRALGEYLEKRQSLQGLVVLM
DIRHPLKDLDQQMIEWAVDSNIAVLVLLTKADKLASGARKAQLNMVREAV
LAFNGDVQVETFSSLKKQGVDKLRQKLDTWFSE

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

Best alignment:
1PUI.pdb     9  RHLPSDTGIEVAFAGRSNAGKSSALNTLTN    38
                + L +      +F   S AG+S  L ++ N
2-10550     17  KRLKASPSSSSSFPAVSVAGRSRDLGSVAN    46

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

Highlighted IDENTICAL residue THR   25  index1   15  path   23  %Seq 100.00
Highlighted IDENTICAL residue GLY   26  index1   16  path   24  %Seq 100.00
Highlighted IDENTICAL residue ALA   30  index1   20  path   28  %Seq  50.00
Highlighted IDENTICAL residue PHE   31  index1   21  path   29  %Seq  50.00
Highlighted IDENTICAL residue ARG   34  index1   24  path   32  %Seq 100.00
Highlighted IDENTICAL residue ALA   37  index1   27  path   35  %Seq 100.00
Highlighted IDENTICAL residue GLY   38  index1   28  path   36  %Seq 100.00
Highlighted IDENTICAL residue LYS   39  index1   29  path   37  %Seq 100.00
Highlighted IDENTICAL residue SER   40  index1   30  path   38  %Seq 100.00
Highlighted IDENTICAL residue LEU   43  index1   33  path   46  %Seq 100.00
Highlighted IDENTICAL residue ASN   48  index1   38  path   51  %Seq 100.00
Highlighted 11 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10550-c1pia_.pir.txt.1PUI.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10550-c1pia_.pir.txt PIR amino_acid 1PUI.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.