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
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/At2g03740-2ch7A0.pir.txt

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

Assigned types to 189 residues in Sequence 2-03740, 8 remain unknown
Assigned types to 309 residues in Sequence 2ch7A0, 42 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 At2g03740-2ch7A0.pir.txt into sequence alignment.

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

>2CH7.pdb  Made from 4630 ATOM records in 2CH7.pdb
GSHMKDVQTETFSVAESIEEISKANEEITNQLLGISKEMDNISTRIESIS
ASVQETTAGSEEISSATKNIADSAQQAASFADQSTQLAKEAGDALKKVIE
VTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNLLALNAAIE
AARAGEAGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSIAEDAGKVS
SEITARVEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAIEEQTAAVD
EITTAMTENAKNAEEITNSVKEVNARLQEISASTEEVTSRVQTIRENVQM
LKEIVARYKSHMKDVQTETFSVAESIEEISKANEEITNQLLGISKEMDNI
STRIESISASVQETTAGSEEISSATKNIADSAQQAASFADQSTQLAKEAG
DALKKVIEVTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNL
LALNAAIEAARAGEAGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSI
AEDAGKVSSEITARVEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAI
EEQNAAVDEITTAMTENAKNAEEITNSVKEVNARLQEISASTEEVTSRVQ
TIRENVQMLKEIVARYK

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

Best alignment:
2CH7.pdb   157  AGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSIAEDAGKVSSEITAR   206
                A +G     ++ + L + S++AS  V+   +E+ +++   G+       R
2-03740     51  AVKGAGNSPNDPKWLDDASEKASGYVKEKGSEVGNVSAQKGQELQNQMER   100

2CH7.pdb   207  VEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAI-EEQTAAVDEITTA   255
                 ++   +  +A E ++S+    +R ++ +      + EE T+  D+    
2-03740    101  AKD--YIFGKAGEAMDSVAENAKRASDFVTEKGKEVKEETTSRTDKAKDF   148

2CH7.pdb   256  MTENAKNAEEITNSVKEVNAR   276
                + E A + ++    ++   ++
2-03740    149  IVEKAGDVKDTAMDMRNKTSK   169

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

Highlighted IDENTICAL residue LEU  391  index1  171  path   71  %Seq 100.00
Highlighted IDENTICAL residue SER  395  index1  175  path   75  %Seq 100.00
Highlighted IDENTICAL residue ARG  404  index1  184  path   86  %Seq 100.00
Highlighted IDENTICAL residue ASN  407  index1  187  path   89  %Seq 100.00
Highlighted IDENTICAL residue VAL  419  index1  199  path  101  %Seq 100.00
Highlighted IDENTICAL residue GLU  429  index1  209  path  111  %Seq 100.00
Highlighted IDENTICAL residue GLU  436  index1  216  path  116  %Seq  50.00
Highlighted IDENTICAL residue ALA  437  index1  217  path  117  %Seq 100.00
Highlighted IDENTICAL residue ASN  442  index1  222  path  122  %Seq 100.00
Highlighted IDENTICAL residue VAL  448  index1  228  path  128  %Seq 100.00
Highlighted IDENTICAL residue GLU  449  index1  229  path  129  %Seq 100.00
Highlighted IDENTICAL residue ILE  451  index1  231  path  131  %Seq 100.00
Highlighted IDENTICAL residue GLU  453  index1  233  path  133  %Seq 100.00
Highlighted IDENTICAL residue ASN  457  index1  237  path  137  %Seq  50.00
Highlighted IDENTICAL residue ILE  458  index1  238  path  138  %Seq 100.00
Highlighted IDENTICAL residue ALA  461  index1  241  path  141  %Seq 100.00
Highlighted IDENTICAL residue ILE  462  index1  242  path  142  %Seq 100.00
Highlighted IDENTICAL residue THR  477  index1  257  path  158  %Seq  50.00
Highlighted IDENTICAL residue GLU  478  index1  258  path  159  %Seq 100.00
Highlighted 19 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03740-2ch7A0.pir.txt.2CH7.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03740-2ch7A0.pir.txt PIR amino_acid 2CH7.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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