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
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
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/At2g06040-c1fzta_.pir.txt

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

Assigned types to 461 residues in Sequence 2-06040, 14 remain unknown
Assigned types to 211 residues in Sequence c1fzta_, 264 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 At2g06040-c1fzta_.pir.txt into sequence alignment.

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

>1FZT.pdb  Made from 3382 ATOM records in 1FZT.pdb
MTTEAAPNLLVLTRHGESEWNKLNLFTGWKDPALSETGIKEAKLGGERLK
SRGYKFDIAFTSALQRAQKTCQIILEEVGEPNLETIKSEKLNERYYGDLQ
GLNKDDARKKWGAEQVQIWRRSYDIAPPNGESLKDTAERVLPYYKSTIVP
HILKGEKVLIAAHGNSLRALIMDLEGLTGDQIVKRELATGVPIVYHLDKD
GKYVSKELIDN

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

Best alignment:
1FZT.pdb    36  ETGIKEAKLG---GERLKSRGYKFDIAFTSALQRAQKTCQIILEEVGEPN    82
                 +G + AK G   G  ++S  + FD+    +  + ++ C  ++EE    N
2-06040     89  RSGKRVAKRGVDYGIEIESSKFDFDLKLGESASKTKRVCVDLVEETIVKN   138

1FZT.pdb    83  LETIKSEKLNERYYGDLQGLNKDDARKKWGAEQVQ   117
                 E+  S  L ++      G+  D   +KW   +V+
2-06040    138  -ESEDSVDLEDK---SSSGVLGDSLAEKWYVVEVE   169

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

Highlighted IDENTICAL residue GLU   36  index1   36  path   89  %Seq  50.00
Highlighted IDENTICAL residue THR   37  index1   37  path   90  %Seq  50.00
Highlighted IDENTICAL residue GLY   38  index1   38  path   91  %Seq  50.00
Highlighted IDENTICAL residue ILE   39  index1   39  path   92  %Seq  50.00
Highlighted IDENTICAL residue LYS   40  index1   40  path   93  %Seq  50.00
Highlighted IDENTICAL residue GLU   41  index1   41  path   94  %Seq  50.00
Highlighted IDENTICAL residue ALA   42  index1   42  path   95  %Seq  50.00
Highlighted IDENTICAL residue LYS   43  index1   43  path   96  %Seq  50.00
Highlighted IDENTICAL residue LEU   44  index1   44  path   97  %Seq  50.00
Highlighted IDENTICAL residue GLY   45  index1   45  path   98  %Seq  50.00
Highlighted IDENTICAL residue GLY   46  index1   46  path  102  %Seq  50.00
Highlighted IDENTICAL residue GLU   47  index1   47  path  103  %Seq  50.00
Highlighted IDENTICAL residue ARG   48  index1   48  path  104  %Seq  50.00
Highlighted IDENTICAL residue LEU   49  index1   49  path  105  %Seq  50.00
Highlighted IDENTICAL residue LYS   50  index1   50  path  106  %Seq  50.00
Highlighted IDENTICAL residue SER   51  index1   51  path  107  %Seq  50.00
Highlighted IDENTICAL residue ARG   52  index1   52  path  108  %Seq  50.00
Highlighted IDENTICAL residue GLY   53  index1   53  path  109  %Seq  50.00
Highlighted IDENTICAL residue TYR   54  index1   54  path  110  %Seq  50.00
Highlighted IDENTICAL residue LYS   55  index1   55  path  111  %Seq  50.00
Highlighted IDENTICAL residue PHE   56  index1   56  path  112  %Seq  50.00
Highlighted IDENTICAL residue ASP   57  index1   57  path  113  %Seq  50.00
Highlighted IDENTICAL residue ILE   58  index1   58  path  114  %Seq  50.00
Highlighted IDENTICAL residue ALA   59  index1   59  path  115  %Seq  50.00
Highlighted IDENTICAL residue PHE   60  index1   60  path  116  %Seq  50.00
Highlighted IDENTICAL residue THR   61  index1   61  path  117  %Seq  50.00
Highlighted IDENTICAL residue SER   62  index1   62  path  118  %Seq  50.00
Highlighted IDENTICAL residue ALA   63  index1   63  path  119  %Seq  50.00
Highlighted IDENTICAL residue LEU   64  index1   64  path  120  %Seq  50.00
Highlighted IDENTICAL residue GLN   65  index1   65  path  121  %Seq  50.00
Highlighted IDENTICAL residue ARG   66  index1   66  path  122  %Seq  50.00
Highlighted IDENTICAL residue ALA   67  index1   67  path  123  %Seq  50.00
Highlighted IDENTICAL residue GLN   68  index1   68  path  124  %Seq  50.00
Highlighted IDENTICAL residue LYS   69  index1   69  path  125  %Seq  50.00
Highlighted IDENTICAL residue THR   70  index1   70  path  126  %Seq  50.00
Highlighted IDENTICAL residue CYS   71  index1   71  path  127  %Seq  50.00
Highlighted IDENTICAL residue GLN   72  index1   72  path  128  %Seq  50.00
Highlighted IDENTICAL residue ILE   73  index1   73  path  129  %Seq  50.00
Highlighted IDENTICAL residue ILE   74  index1   74  path  130  %Seq  50.00
Highlighted IDENTICAL residue LEU   75  index1   75  path  131  %Seq  50.00
Highlighted IDENTICAL residue GLU   76  index1   76  path  132  %Seq  50.00
Highlighted IDENTICAL residue GLU   77  index1   77  path  133  %Seq  50.00
Highlighted IDENTICAL residue VAL   78  index1   78  path  134  %Seq  50.00
Highlighted IDENTICAL residue GLY   79  index1   79  path  135  %Seq  50.00
Highlighted IDENTICAL residue GLU   80  index1   80  path  136  %Seq  50.00
Highlighted IDENTICAL residue PRO   81  index1   81  path  137  %Seq  50.00
Highlighted IDENTICAL residue ASN   82  index1   82  path  138  %Seq  50.00
Highlighted IDENTICAL residue GLU   84  index1   84  path  139  %Seq  50.00
Highlighted IDENTICAL residue THR   85  index1   85  path  140  %Seq  50.00
Highlighted IDENTICAL residue ILE   86  index1   86  path  141  %Seq  50.00
Highlighted IDENTICAL residue LYS   87  index1   87  path  142  %Seq  50.00
Highlighted IDENTICAL residue SER   88  index1   88  path  143  %Seq  50.00
Highlighted IDENTICAL residue GLU   89  index1   89  path  144  %Seq  50.00
Highlighted IDENTICAL residue LYS   90  index1   90  path  145  %Seq  50.00
Highlighted IDENTICAL residue LEU   91  index1   91  path  146  %Seq  50.00
Highlighted IDENTICAL residue ASN   92  index1   92  path  147  %Seq  50.00
Highlighted IDENTICAL residue GLU   93  index1   93  path  148  %Seq  50.00
Highlighted IDENTICAL residue ARG   94  index1   94  path  149  %Seq  50.00
Highlighted IDENTICAL residue ASP   98  index1   98  path  150  %Seq  50.00
Highlighted IDENTICAL residue LEU   99  index1   99  path  151  %Seq  50.00
Highlighted IDENTICAL residue GLN  100  index1  100  path  152  %Seq  50.00
Highlighted IDENTICAL residue GLY  101  index1  101  path  153  %Seq  50.00
Highlighted IDENTICAL residue LEU  102  index1  102  path  154  %Seq  50.00
Highlighted IDENTICAL residue ASN  103  index1  103  path  155  %Seq  50.00
Highlighted IDENTICAL residue LYS  104  index1  104  path  156  %Seq  50.00
Highlighted IDENTICAL residue ASP  105  index1  105  path  157  %Seq  50.00
Highlighted IDENTICAL residue ASP  106  index1  106  path  158  %Seq  50.00
Highlighted IDENTICAL residue ALA  107  index1  107  path  159  %Seq  50.00
Highlighted IDENTICAL residue ARG  108  index1  108  path  160  %Seq  50.00
Highlighted IDENTICAL residue LYS  109  index1  109  path  161  %Seq  50.00
Highlighted IDENTICAL residue LYS  110  index1  110  path  162  %Seq  50.00
Highlighted IDENTICAL residue TRP  111  index1  111  path  163  %Seq  50.00
Highlighted IDENTICAL residue GLY  112  index1  112  path  164  %Seq  50.00
Highlighted IDENTICAL residue ALA  113  index1  113  path  165  %Seq  50.00
Highlighted IDENTICAL residue GLU  114  index1  114  path  166  %Seq  50.00
Highlighted IDENTICAL residue GLN  115  index1  115  path  167  %Seq  50.00
Highlighted IDENTICAL residue VAL  116  index1  116  path  168  %Seq  50.00
Highlighted IDENTICAL residue GLN  117  index1  117  path  169  %Seq  50.00
Highlighted 78 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g06040-c1fzta_.pir.txt.1FZT.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g06040-c1fzta_.pir.txt PIR amino_acid 1FZT.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.