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/At2g03540-1ji6A.pir.txt

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

Assigned types to 166 residues in Sequence 2-03540, 2 remain unknown
Assigned types to 102 residues in Sequence 1ji6A, 66 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 At2g03540-1ji6A.pir.txt into sequence alignment.

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

>1JI6.pdb  Made from 4750 ATOM records in 1JI6.pdb
DAVGTGISVVGQILGVVGVPFAGALTSFYQSFLNTIWPSDADPWKAFMAQ
VEVLIDKKIEEYAKSKALAELQGLQNNFEDYVNALNSWKKTPLSLRSKRS
QDRIRELFSQAESHFRNSMPSFAVSKFEVLFLPTYAQAANTHLLLLKDAQ
VFGEEWGYSSEDVAEFYHRQLKLTQQYTDHCVNWYNVGLNGLRGSTYDAW
VKFNRFRREMTLTVLDLIVLFPFYDIRLYSKGVKTELTRDIFTDPIFSLN
TLQEYGPTFLSIENSIRKPHLFDYLQGIEFHTRLQPGYFGKDSFNYWSGN
YVETRPSIGSSKTITSPFYGDKSTEPVQKLSFDGQKVYRTIANTDVAAWP
NGKVYLGVTKVDFSQYDDQKNETSTQTYDSKRNNGHVSAQDSIDQLPPET
TDEPLEKAYSHQLNYAECFLMQDRRGTIPFFTWTHRSVDFFNTIDAEKIT
QLPVVKAYALSSGASIIEGPGFTGGNLLFLKESSNSIAKFKVTLNSAALL
QRYRVRIRYASTTNLRLFVQNSNNDFLVIYINKTMNKDDDLTYQTFDLAT
TNSNMGFSGDKNELIIGAESFVSNEKIYIDKIEFIPVQL

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

Best alignment:
1JI6.pdb    82  VNALNSWKKTPLSLRSKRSQDRIRELF----SQAESHFRNSMPSFAVSK   126
                V+ L S ++     R+ R+ ++ R L+       ESH  N    F   K
2-03540     26  VDCLRSMEEMLALKRNSRTNEQDRVLWKGKNGHLESHTHNGEQGFLAQK    74

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

Highlighted IDENTICAL residue VAL  145  index1   82  path   26  %Seq  50.00
Highlighted IDENTICAL residue ASN  146  index1   83  path   27  %Seq  50.00
Highlighted IDENTICAL residue ALA  147  index1   84  path   28  %Seq  50.00
Highlighted IDENTICAL residue LEU  148  index1   85  path   29  %Seq  50.00
Highlighted IDENTICAL residue ASN  149  index1   86  path   30  %Seq  50.00
Highlighted IDENTICAL residue SER  150  index1   87  path   31  %Seq  50.00
Highlighted IDENTICAL residue TRP  151  index1   88  path   32  %Seq  50.00
Highlighted IDENTICAL residue LYS  152  index1   89  path   33  %Seq  50.00
Highlighted IDENTICAL residue LYS  153  index1   90  path   34  %Seq  50.00
Highlighted IDENTICAL residue THR  154  index1   91  path   35  %Seq  50.00
Highlighted IDENTICAL residue PRO  155  index1   92  path   36  %Seq  50.00
Highlighted IDENTICAL residue LEU  156  index1   93  path   37  %Seq  50.00
Highlighted IDENTICAL residue SER  157  index1   94  path   38  %Seq  50.00
Highlighted IDENTICAL residue LEU  158  index1   95  path   39  %Seq  50.00
Highlighted IDENTICAL residue ARG  159  index1   96  path   40  %Seq  50.00
Highlighted IDENTICAL residue SER  160  index1   97  path   41  %Seq  50.00
Highlighted IDENTICAL residue LYS  161  index1   98  path   42  %Seq  50.00
Highlighted IDENTICAL residue ARG  162  index1   99  path   43  %Seq  50.00
Highlighted IDENTICAL residue SER  163  index1  100  path   44  %Seq  50.00
Highlighted IDENTICAL residue GLN  164  index1  101  path   45  %Seq  50.00
Highlighted IDENTICAL residue ASP  165  index1  102  path   46  %Seq  50.00
Highlighted IDENTICAL residue ARG  166  index1  103  path   47  %Seq  50.00
Highlighted IDENTICAL residue ILE  167  index1  104  path   48  %Seq  50.00
Highlighted IDENTICAL residue ARG  168  index1  105  path   49  %Seq  50.00
Highlighted IDENTICAL residue GLU  169  index1  106  path   50  %Seq  50.00
Highlighted IDENTICAL residue LEU  170  index1  107  path   51  %Seq  50.00
Highlighted IDENTICAL residue PHE  171  index1  108  path   52  %Seq  50.00
Highlighted IDENTICAL residue SER  172  index1  109  path   57  %Seq  50.00
Highlighted IDENTICAL residue GLN  173  index1  110  path   58  %Seq  50.00
Highlighted IDENTICAL residue ALA  174  index1  111  path   59  %Seq  50.00
Highlighted IDENTICAL residue GLU  175  index1  112  path   60  %Seq  50.00
Highlighted IDENTICAL residue SER  176  index1  113  path   61  %Seq  50.00
Highlighted IDENTICAL residue HIS  177  index1  114  path   62  %Seq  50.00
Highlighted 33 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03540-1ji6A.pir.txt.1JI6.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03540-1ji6A.pir.txt PIR amino_acid 1JI6.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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