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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14750-1i2d_A.pir.txt

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

Assigned types to 276 residues in Sequence 2-14750, 20 remain unknown
Assigned types to 271 residues in Sequence 1i2d_A, 25 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 11  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 12  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 13  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 14  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 15  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 16  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 17  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 18  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 19  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 20  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 73  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 74  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 75  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 76  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 77  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 78  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 79  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 80  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 152  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 219  All residues are positively and negatively charged

Translated sequence file At2g14750-1i2d_A.pir.txt into sequence alignment.

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

>1I2D.pdb  Made from 13407 ATOM records in 1I2D.pdb
ANAPHGGVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGG
FSPLEGFMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAGS
RITLRDFRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTV
KEFYIGGKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNP
MHRAHRELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRY
PNGMAVLGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNS
KGEDFYGPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAG
VKTLNISGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFL
TGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDR
HTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVH
VATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQ
SVRSIVHEIILVLESQGFLERQANAPHGGVLKDLLARDAPRQAELAAEAE
SLPAVTLTERQLCDLELIMNGGFSPLEGFMNQADYDRVCEDNRLADGNVF
SMPITLDASQEVIDEKKLQAGSRITLRDFRDDRNLAILTIDDIYRPDKTK
EAKLVFGGDPEHPAIVYLNNTVKEFYIGGKIEAVNKLNHYDYVALRYTPA
ELRVHFDKLGWSRVVAFQTRNPMHRAHRELTVRAARSRQANVLIHPVVGL
TKPGDIDHFTRVRAYQALLPRYPNGMAVLGLLGLAMRMGGPREAIWHAII
RKNHGATHFIVGRDHAGPGSNSKGEDFYGPYDAQHAVEKYKDELGIEVVE
FQMVTYLPDTDEYRPVDQVPAGVKTLNISGTELRRRLRSGAHIPEWFSYP
EVVKILRESNPPRATQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVS
LLLGDTVRHELSSELGFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAP
YEESRKFARDAVSQAGSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGF
TGVDDPYETPEKADLVVDFSKQSVRSIVHEIILVLESQGFLERQANAPHG
GVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGGFSPLEG
FMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAGSRITLRD
FRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTVKEFYIG
GKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNPMHRAHR
ELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRYPNGMAV
LGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNSKGEDFY
GPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAGVKTLNI
SGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFLTGYMNS
GKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDRHTNIQR
IAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVHVATPLE
HCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQSVRSIV
HEIILVLESQGFLERQ

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

Best alignment:
1I2D.pdb   394  QGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSEL   443
                +G  I++TG   SGK  +A AL   L Q+ G+   +L GD VRH L+ +L
2-14750    100  KGCVIWVTGLSGSGKSTLACALNQMLYQK-GKLCYILDGDNVRHGLNRDL   148

1I2D.pdb   444  GFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQA   493
                 F  EDR  NI+R+  VA     AG   IA+ I+PY   R   R  + + 
2-14750    149  SFKAEDRAENIRRVGEVAKLFADAGIICIASLISPYRTDRDACRSLLPE-   197

1I2D.pdb   494  GSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADL   543
                G F  V +  PL  CE  D +G+Y  AR G+IKGFTG+DDPYE P   ++
2-14750    198  GDFVEVFMDVPLSVCEARDPKGLYKLARAGKIKGFTGIDDPYEPPLNCEI   247

1I2D.pdb   544  VVD-FSKQSVRSIVHEIILVLESQGFLE   570
                 +      S   +  +++  L+++G+L+
2-14750    248  SLGREGGTSPIEMAEKVVGYLDNKGYLQ   275

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

Highlighted IDENTICAL residue GLY  396  index1  395  path  119  %Seq 100.00
Highlighted IDENTICAL residue ILE  399  index1  398  path  122  %Seq 100.00
Highlighted IDENTICAL residue THR  402  index1  401  path  125  %Seq 100.00
Highlighted IDENTICAL residue GLY  403  index1  402  path  126  %Seq 100.00
Highlighted IDENTICAL residue SER  407  index1  406  path  130  %Seq 100.00
Highlighted IDENTICAL residue GLY  408  index1  407  path  131  %Seq 100.00
Highlighted IDENTICAL residue LYS  409  index1  408  path  132  %Seq 100.00
Highlighted IDENTICAL residue ALA  413  index1  412  path  136  %Seq 100.00
Highlighted IDENTICAL residue ALA  415  index1  414  path  138  %Seq 100.00
Highlighted IDENTICAL residue LEU  416  index1  415  path  139  %Seq 100.00
Highlighted IDENTICAL residue LEU  420  index1  419  path  143  %Seq 100.00
Highlighted IDENTICAL residue GLN  422  index1  421  path  145  %Seq 100.00
Highlighted IDENTICAL residue GLY  425  index1  424  path  147  %Seq 100.00
Highlighted IDENTICAL residue LEU  431  index1  430  path  154  %Seq 100.00
Highlighted IDENTICAL residue GLY  433  index1  432  path  156  %Seq 100.00
Highlighted IDENTICAL residue ASP  434  index1  433  path  157  %Seq 100.00
Highlighted IDENTICAL residue VAL  436  index1  435  path  159  %Seq 100.00
Highlighted IDENTICAL residue ARG  437  index1  436  path  160  %Seq 100.00
Highlighted IDENTICAL residue HIS  438  index1  437  path  161  %Seq 100.00
Highlighted IDENTICAL residue LEU  440  index1  439  path  163  %Seq 100.00
Highlighted IDENTICAL residue LEU  444  index1  443  path  167  %Seq 100.00
Highlighted IDENTICAL residue PHE  446  index1  445  path  169  %Seq 100.00
Highlighted IDENTICAL residue GLU  449  index1  448  path  172  %Seq 100.00
Highlighted IDENTICAL residue ASP  450  index1  449  path  173  %Seq 100.00
Highlighted IDENTICAL residue ARG  451  index1  450  path  174  %Seq 100.00
Highlighted IDENTICAL residue ASN  454  index1  453  path  177  %Seq 100.00
Highlighted IDENTICAL residue ILE  455  index1  454  path  178  %Seq 100.00
Highlighted IDENTICAL residue ARG  457  index1  456  path  180  %Seq 100.00
Highlighted IDENTICAL residue VAL  461  index1  460  path  184  %Seq 100.00
Highlighted IDENTICAL residue ALA  462  index1  461  path  185  %Seq 100.00
Highlighted IDENTICAL residue ALA  468  index1  467  path  191  %Seq 100.00
Highlighted IDENTICAL residue GLY  469  index1  468  path  192  %Seq 100.00
Highlighted IDENTICAL residue ILE  473  index1  472  path  196  %Seq 100.00
Highlighted IDENTICAL residue ALA  474  index1  473  path  197  %Seq 100.00
Highlighted IDENTICAL residue ILE  477  index1  476  path  200  %Seq 100.00
Highlighted IDENTICAL residue PRO  479  index1  478  path  202  %Seq 100.00
Highlighted IDENTICAL residue TYR  480  index1  479  path  203  %Seq 100.00
Highlighted IDENTICAL residue ARG  484  index1  483  path  207  %Seq 100.00
Highlighted IDENTICAL residue ARG  488  index1  487  path  211  %Seq 100.00
Highlighted IDENTICAL residue PHE  497  index1  496  path  220  %Seq 100.00
Highlighted IDENTICAL residue VAL  500  index1  499  path  223  %Seq 100.00
Highlighted IDENTICAL residue PRO  505  index1  504  path  228  %Seq 100.00
Highlighted IDENTICAL residue LEU  506  index1  505  path  229  %Seq 100.00
Highlighted IDENTICAL residue CYS  509  index1  508  path  232  %Seq 100.00
Highlighted IDENTICAL residue GLU  510  index1  509  path  233  %Seq 100.00
Highlighted IDENTICAL residue ASP  513  index1  512  path  236  %Seq 100.00
Highlighted IDENTICAL residue GLY  516  index1  515  path  239  %Seq 100.00
Highlighted IDENTICAL residue TYR  518  index1  517  path  241  %Seq 100.00
Highlighted IDENTICAL residue ALA  521  index1  520  path  244  %Seq 100.00
Highlighted IDENTICAL residue ARG  522  index1  521  path  245  %Seq 100.00
Highlighted IDENTICAL residue GLY  524  index1  523  path  247  %Seq 100.00
Highlighted IDENTICAL residue ILE  526  index1  525  path  249  %Seq 100.00
Highlighted IDENTICAL residue LYS  527  index1  526  path  250  %Seq 100.00
Highlighted IDENTICAL residue GLY  528  index1  527  path  251  %Seq 100.00
Highlighted IDENTICAL residue PHE  529  index1  528  path  252  %Seq 100.00
Highlighted IDENTICAL residue THR  530  index1  529  path  253  %Seq 100.00
Highlighted IDENTICAL residue GLY  531  index1  530  path  254  %Seq 100.00
Highlighted IDENTICAL residue ASP  533  index1  532  path  256  %Seq 100.00
Highlighted IDENTICAL residue ASP  534  index1  533  path  257  %Seq 100.00
Highlighted IDENTICAL residue PRO  535  index1  534  path  258  %Seq 100.00
Highlighted IDENTICAL residue TYR  536  index1  535  path  259  %Seq 100.00
Highlighted IDENTICAL residue GLU  537  index1  536  path  260  %Seq 100.00
Highlighted IDENTICAL residue PRO  539  index1  538  path  262  %Seq 100.00
Highlighted IDENTICAL residue SER  549  index1  548  path  273  %Seq  50.00
Highlighted IDENTICAL residue SER  552  index1  551  path  276  %Seq 100.00
Highlighted IDENTICAL residue LEU  564  index1  563  path  288  %Seq 100.00
Highlighted IDENTICAL residue GLY  568  index1  567  path  292  %Seq 100.00
Highlighted IDENTICAL residue LEU  570  index1  569  path  294  %Seq 100.00
Highlighted 68 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14750-1i2d_A.pir.txt.1I2D.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14750-1i2d_A.pir.txt PIR amino_acid 1I2D.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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