&&&&&&&&&&&&&&&&&&&& 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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