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/At2g11910-1ux6A.pir.txt

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

Assigned types to 168 residues in Sequence 2-11910, 17 remain unknown
Assigned types to 91 residues in Sequence 1ux6A, 94 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 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 81  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 82  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 83  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 84  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 95  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 113  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 114  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 115  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 155  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 156  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 157  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 158  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 159  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 160  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 161  All residues are positively and negatively charged

Translated sequence file At2g11910-1ux6A.pir.txt into sequence alignment.

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

>1UX6.pdb  Made from 2667 ATOM records in 1UX6.pdb
ALADNCPLEHNPDQLDSDSDRIGDTCDNNQDIDEDGHQNNLDNCPYVPNA
NQADHDKDGKGDACDHDDDNDGIPDDKDNCRLVPNPDQKDSDGDGRGDAC
KDDFDHDSVPDIDDICPENVDISETDFRRFQMIPLDPKGTSQNDPNWVVE
LVQTVNSDPGLAVGYDEFNAVDFSGTFFINTERDDDYAGFVFGYQSSSRF
YVVMWKQVTQSYWDTNPTRAQGYSGLSVKVVKSTTGPGEHLRNALWHTGN
TPGQVRTLWHDPRHIGWKDFTAYRWRLSHRPKTGFIRVVMYEGKKIMADS
GPIYDKTYAGGRLGLFVFSQEMVFFSDLKYECRDP

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

Best alignment:
1UX6.pdb     8  LEHNPDQLDSDSDRIGDTCDNNQDIDEDGHQNNLDNCPYVPNANQADHDK    57
                +E N D  DSD D   +  D + D ++D +  +           +AD + 
2-11910     66  IEENKDASDSDDDDDDEDADEDDDDEDDANDEDFSGGEGDEGEEEADPED   115

1UX6.pdb    58  D-----GKGDACDHDDDNDGIPDDKDNCRLVPNPDQKDSDGD    94
                D     G G   + DDD +G  DD+D        D  + D D
2-11910    116  DPVTNGGGGSDDEDDDDEEGDNDDEDEDNEDEEEDDDEEDDD   157

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

Highlighted IDENTICAL residue GLU  821  index1    9  path   67  %Seq 100.00
Highlighted IDENTICAL residue ASN  823  index1   11  path   69  %Seq 100.00
Highlighted IDENTICAL residue ASP  825  index1   13  path   71  %Seq 100.00
Highlighted IDENTICAL residue ASP  828  index1   16  path   74  %Seq 100.00
Highlighted IDENTICAL residue SER  829  index1   17  path   75  %Seq 100.00
Highlighted IDENTICAL residue ASP  830  index1   18  path   76  %Seq 100.00
Highlighted IDENTICAL residue ASP  832  index1   20  path   78  %Seq 100.00
Highlighted IDENTICAL residue ARG  833  index1   21  path   85  %Seq 100.00
Highlighted IDENTICAL residue THR  837  index1   25  path   89  %Seq 100.00
Highlighted IDENTICAL residue ASP  839  index1   27  path   91  %Seq 100.00
Highlighted IDENTICAL residue ASN  840  index1   28  path   92  %Seq 100.00
Highlighted IDENTICAL residue ASN  841  index1   29  path   93  %Seq 100.00
Highlighted IDENTICAL residue ASP  847  index1   35  path  100  %Seq 100.00
Highlighted IDENTICAL residue VAL  859  index1   47  path  112  %Seq 100.00
Highlighted IDENTICAL residue ASN  861  index1   49  path  117  %Seq 100.00
Highlighted IDENTICAL residue ALA  865  index1   53  path  121  %Seq 100.00
Highlighted IDENTICAL residue LYS  869  index1   57  path  125  %Seq 100.00
Highlighted IDENTICAL residue ASP  870  index1   58  path  126  %Seq 100.00
Highlighted IDENTICAL residue LYS  872  index1   60  path  133  %Seq 100.00
Highlighted IDENTICAL residue ALA  875  index1   63  path  136  %Seq 100.00
Highlighted IDENTICAL residue CYS  876  index1   64  path  137  %Seq 100.00
Highlighted IDENTICAL residue HIS  878  index1   66  path  139  %Seq 100.00
Highlighted IDENTICAL residue ASP  887  index1   75  path  148  %Seq 100.00
Highlighted IDENTICAL residue ASP  890  index1   78  path  151  %Seq 100.00
Highlighted IDENTICAL residue CYS  892  index1   80  path  153  %Seq 100.00
Highlighted IDENTICAL residue VAL  895  index1   83  path  163  %Seq 100.00
Highlighted IDENTICAL residue GLN  900  index1   88  path  168  %Seq 100.00
Highlighted IDENTICAL residue ASP  904  index1   92  path  172  %Seq 100.00
Highlighted IDENTICAL residue ASP  906  index1   94  path  174  %Seq 100.00
Highlighted 29 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g11910-1ux6A.pir.txt.1UX6.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g11910-1ux6A.pir.txt PIR amino_acid 1UX6.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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