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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04530-2cbnA.pir.txt

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

Assigned types to 354 residues in Sequence 2-4530, 28 remain unknown
Assigned types to 299 residues in Sequence 2cbnA, 83 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 At2g04530-2cbnA.pir.txt into sequence alignment.

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

>2CBN.pdb  Made from 2267 ATOM records in 2CBN.pdb
AMNLIFLGTSAGVPTRTRNVTAILLNLQHPTQSGLWLFDCGEGTQHQLLH
TAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIRE
FVETALRISGSWTDYPLEIVEIGAGEILDDGLRKVTAYPLEHPLECYGYR
IEEHDAPGALNAQALKAAGVPPGPLFQELKAGKTITLEDGRQINGADYLA
APVPGKALAIFGDTGPCDAALDLAKGVDVMVHEATLDITMEAKANSRGHS
STRQAATLAREAGVGKLIITHVSSRYDDKGCQHLLRECRSIFPATELAND
FTVFNV

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

Best alignment:
2CBN.pdb    61  IFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIREFVETALRISG   110
                +FI+H H DH+ GLP  + SR +   ++P  I+ P  I+E VE  L I  
2-4530     119  LFITHAHLDHIGGLPMYVASRGLYN-LEPPKIFVPPSIKEDVEKLLEIHR   167

2CBN.pdb   111  SW--TDYPLEIVEIGAGE   126
                +    +  +E++ +  GE
2-4530     168  TMGQVELNVELIPLAVGE   185

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

Highlighted IDENTICAL residue PHE   61  index1   62  path  128  %Seq 100.00
Highlighted IDENTICAL residue ILE   62  index1   63  path  129  %Seq 100.00
Highlighted IDENTICAL residue HIS   64  index1   65  path  131  %Seq 100.00
Highlighted IDENTICAL residue HIS   66  index1   67  path  133  %Seq 100.00
Highlighted IDENTICAL residue ASP   68  index1   69  path  135  %Seq 100.00
Highlighted IDENTICAL residue HIS   69  index1   70  path  136  %Seq 100.00
Highlighted IDENTICAL residue GLY   72  index1   73  path  139  %Seq 100.00
Highlighted IDENTICAL residue LEU   73  index1   74  path  140  %Seq 100.00
Highlighted IDENTICAL residue PRO   74  index1   75  path  141  %Seq 100.00
Highlighted IDENTICAL residue SER   79  index1   80  path  146  %Seq 100.00
Highlighted IDENTICAL residue ARG   80  index1   81  path  147  %Seq 100.00
Highlighted IDENTICAL residue PRO   88  index1   89  path  155  %Seq 100.00
Highlighted IDENTICAL residue ILE   91  index1   92  path  158  %Seq 100.00
Highlighted IDENTICAL residue PRO   94  index1   95  path  161  %Seq 100.00
Highlighted IDENTICAL residue ILE   97  index1   98  path  164  %Seq 100.00
Highlighted IDENTICAL residue GLU   99  index1  100  path  166  %Seq 100.00
Highlighted IDENTICAL residue VAL  101  index1  102  path  168  %Seq 100.00
Highlighted IDENTICAL residue GLU  102  index1  103  path  169  %Seq 100.00
Highlighted IDENTICAL residue LEU  105  index1  106  path  172  %Seq 100.00
Highlighted IDENTICAL residue ILE  107  index1  108  path  174  %Seq 100.00
Highlighted IDENTICAL residue TYR  114  index1  115  path  183  %Seq 100.00
Highlighted IDENTICAL residue VAL  119  index1  120  path  188  %Seq 100.00
Highlighted IDENTICAL residue ILE  121  index1  122  path  190  %Seq  50.00
Highlighted IDENTICAL residue GLY  122  index1  123  path  191  %Seq  50.00
Highlighted IDENTICAL residue ALA  123  index1  124  path  192  %Seq  50.00
Highlighted 25 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04530-2cbnA.pir.txt.2CBN.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04530-2cbnA.pir.txt PIR amino_acid 2CBN.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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