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At2g10070.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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/At2g10070-1-c1ub1a_.pir.txt

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

Assigned types to 150 residues in Sequence 2-10070-150, 28 remain unknown
Assigned types to 125 residues in Sequence c1ub1a_, 53 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 At2g10070-1-c1ub1a_.pir.txt into sequence alignment.

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

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HE2 in residue GLU 77

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 91

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 97

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 98

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HE2 in residue GLU 103

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 122

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HE2 in residue GLU 138

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HE2 in residue GLU 144

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 148

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 152

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 155

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HD2 in residue ASP 157

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom HE2 in residue GLU 170

>1UB1.pdb  Made from 1969 ATOM records in 1UB1.pdb
APAVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKY
DVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRREQ
RPPKKAKSPKSPGSGRGRGRPKGSG

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

Best alignment:
1UB1.pdb        5  PEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKL    38
                   P A   P+ R   +R    +   P   E WT  L
2-10070-150   108  PVADVLPELREDSLRALNDVLQVPG-REAWTTVL   140

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

Highlighted IDENTICAL residue PRO   76  index1    5  path  136  %Seq  50.00
Highlighted IDENTICAL residue GLU   77  index1    6  path  137  %Seq  50.00
Highlighted IDENTICAL residue ALA   78  index1    7  path  138  %Seq  50.00
Highlighted IDENTICAL residue SER   79  index1    8  path  139  %Seq  50.00
Highlighted IDENTICAL residue ALA   80  index1    9  path  140  %Seq  50.00
Highlighted IDENTICAL residue SER   81  index1   10  path  141  %Seq  50.00
Highlighted IDENTICAL residue PRO   82  index1   11  path  142  %Seq  50.00
Highlighted IDENTICAL residue LYS   83  index1   12  path  143  %Seq  50.00
Highlighted IDENTICAL residue GLN   84  index1   13  path  144  %Seq  50.00
Highlighted IDENTICAL residue ARG   85  index1   14  path  145  %Seq  50.00
Highlighted IDENTICAL residue ARG   86  index1   15  path  146  %Seq  50.00
Highlighted IDENTICAL residue SER   87  index1   16  path  147  %Seq  50.00
Highlighted IDENTICAL residue ILE   88  index1   17  path  148  %Seq  50.00
Highlighted IDENTICAL residue ILE   89  index1   18  path  149  %Seq  50.00
Highlighted IDENTICAL residue ARG   90  index1   19  path  150  %Seq  50.00
Highlighted IDENTICAL residue ASP   91  index1   20  path  151  %Seq  50.00
Highlighted IDENTICAL residue ARG   92  index1   21  path  152  %Seq  50.00
Highlighted IDENTICAL residue GLY   93  index1   22  path  153  %Seq  50.00
Highlighted IDENTICAL residue PRO   94  index1   23  path  154  %Seq  50.00
Highlighted IDENTICAL residue MET   95  index1   24  path  155  %Seq  50.00
Highlighted IDENTICAL residue TYR   96  index1   25  path  156  %Seq  50.00
Highlighted IDENTICAL residue ASP   97  index1   26  path  157  %Seq  50.00
Highlighted IDENTICAL residue ASP   98  index1   27  path  158  %Seq  50.00
Highlighted IDENTICAL residue PRO   99  index1   28  path  159  %Seq  50.00
Highlighted IDENTICAL residue THR  100  index1   29  path  160  %Seq  50.00
Highlighted IDENTICAL residue PRO  102  index1   31  path  161  %Seq  50.00
Highlighted IDENTICAL residue GLU  103  index1   32  path  162  %Seq  50.00
Highlighted IDENTICAL residue GLY  104  index1   33  path  163  %Seq  50.00
Highlighted IDENTICAL residue TRP  105  index1   34  path  164  %Seq  50.00
Highlighted IDENTICAL residue THR  106  index1   35  path  165  %Seq  50.00
Highlighted IDENTICAL residue ARG  107  index1   36  path  166  %Seq  50.00
Highlighted IDENTICAL residue LYS  108  index1   37  path  167  %Seq  50.00
Highlighted IDENTICAL residue LEU  109  index1   38  path  168  %Seq  50.00
Highlighted 33 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10070-1-c1ub1a_.pir.txt.1UB1.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10070-1-c1ub1a_.pir.txt PIR amino_acid 1UB1.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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