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/At2g11810-1vgv_A.pir.txt

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

Assigned types to 465 residues in Sequence 2-11810, 21 remain unknown
Assigned types to 354 residues in Sequence 1vgv_A, 132 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 214  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 215  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 216  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 217  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 218  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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 220  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 221  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 222  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 223  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 270  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 271  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 272  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 273  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 274  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 275  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 276  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 277  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 351  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 365  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 366  All residues are positively and negatively charged

Translated sequence file At2g11810-1vgv_A.pir.txt into sequence alignment.

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

>1VGV.pdb  Made from 11450 ATOM records in 1VGV.pdb
KVLTVFGTRPEAIKAPLVHALAKDPFFEAKVCVTAQHRELDQVLKLFSIV
PDYDLNIQPGQGLTEITCRILEGLKPILAEFKPDVVLVHGDTTTTLATSL
AAFYQRIPVGHVEAGLRTGDLYSPWPEEANRTLTGHLAYHFSPTETSRQN
LLRENVADSRIFITGNTVIDALLWVRDQVSSDKLRSELAANYPFIDPDKK
ILVTGHRRESFGRGFEEICHALADIATTHQDIQIVYPVHLNPNVREPVNR
ILGHVKNVILIDPQEYLPFVWLNHAWLILTDSGGIQEEAPSLGKPVLVRD
TTERPEAVTAGTVRLVGTDKQRIVEEVTRLLKDENEYQASRAHNPYGDGQ
ACSRILEALKNNRISLKVLTVFGTRPEAIKAPLVHALAKDPFFEAKVCVT
AQHRELDQVLKLFSIVPDYDLNIQGLTEITCRILEGLKPILAEFKPDVVL
VHGDTTTTLATSLAAFYQRIPVGHVEAGLRTGDLYSPWPEEANRTLTGHL
AYHFSPTETSRQNLLRENVADSRIFITGNTVIDALLWVRDQVSSDKLRSE
LAANYPFIDPDKKILVTGHRRESFGRGFEEICHALADIATTHQDIQIVYP
VHLNPNVREPVNRILGHVKNVILIDPQEYLPFVWLNHAWLILTDSGGIQE
EAPSLGKPVLVRDTTERPEAVTAGTVRLVGTDKQRIVEEVTRLLKDENEY
QASRAHNPYGDGQACSRILEALKNNRISLKVLTVFGTRPEAIKAPLVHAL
AKDPFFEAKVCVTAQHRELDQVLKLFSIVPDYDLNIGQGLTEITCRILEG
LKPILAEFKPDVVLVHGDTTTTLATSLAAFYQRIPVGHVEAGLRTGDLYS
PWPEEANRTLTGHLAYHFSPTETSRQNLLRENVADSRIFITGNTVIDALL
WVRDQVSSDKLRSELAANYPFIDPDKKILVTGHRFGRGFEEICHALADIA
TTHQDIQIVYPVHLNPNVREPVNRILGHVKNVILIDPQEYLPFVWLNHAW
LILTDSGGIQEEAPSLGKPVLVRDTTERPEAVTAGTVRLVGTDKQRIVEE
VTRLLKDENEYQASRAHNPYGDGQACSRILEALKNNRKVLTVFGTRPEAI
KAPLVHALAKDPFFEAKVCVTAQHRELDQVLKLFSIVPDYDLNIQPGQGL
TEITCRILEGLKPILAEFKPDVVLVHGDTTTTLATSLAAFYQRIPVGHVE
AGLRTGDLYSPWPEEANRTLTGHLAYHFSPTETSRQNLLRENVADSRIFI
TGNTVIDALLWVRDQVSSDKLRSELAANYPFIDPDKKILVTGHRRESFGR
GFEEICHALADIATTHQDIQIVYPVHLNPNVREPVNRILGHVKNVILIDP
QEYLPFVWLNHAWLILTDSGGIQEEAPSLGKPVLVRDTTERPEAVTAGTV
RLVGTDKQRIVEEVTRLLKDENEYQASRAHNPYGDGQACSRILEALKNNR
I

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

Best alignment:
1VGV.pdb   271  WLNHAWLILTDSG-GIQEEAPSLGKPVLVRD   300
                W+     I+T +G G   EA   G P+++ D
2-11810    351  WMGACDCIITKAGPGTIAEALICGLPIILND   381

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

Highlighted IDENTICAL residue LEU  279  index1  272  path  373  %Seq 100.00
Highlighted IDENTICAL residue ILE  286  index1  278  path  379  %Seq 100.00
Highlighted IDENTICAL residue THR  288  index1  280  path  381  %Seq 100.00
Highlighted IDENTICAL residue GLY  291  index1  283  path  384  %Seq 100.00
Highlighted IDENTICAL residue GLY  292  index1  284  path  386  %Seq 100.00
Highlighted IDENTICAL residue GLU  296  index1  288  path  390  %Seq 100.00
Highlighted IDENTICAL residue ALA  297  index1  289  path  391  %Seq 100.00
Highlighted IDENTICAL residue GLY  301  index1  293  path  395  %Seq 100.00
Highlighted IDENTICAL residue PRO  303  index1  295  path  397  %Seq 100.00
Highlighted 9 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g11810-1vgv_A.pir.txt.1VGV.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g11810-1vgv_A.pir.txt PIR amino_acid 1VGV.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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