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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01031_1gk4A0.pir.txt

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

Assigned types to 249 residues in Sequence 2-01031, 3 remain unknown
Assigned types to 79 residues in Sequence 1gk4A0, 173 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 At2g01031_1gk4A0.pir.txt into sequence alignment.

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

>1GK4.pdb  Made from 3711 ATOM records in 1GK4.pdb
CEVDALKGTNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMA
RHLREYQDLLNVKMALDIEIATYRKLLEGCEVDALKGTNESLERQMREME
ENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIA
TYRKLLEGNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMAR
HLREYQDLLNVKMALDIEIATYRKLLEGVDALKGTNESLERQMREMEENF
AVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYR
KLLEGENESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMARHL
REYQDLLNVKMALDIEIATYRKLLEGLKGTNESLERQMREMEENFAVEAA
NYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEG

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

Best alignment:
1GK4.pdb   351  REYQDLLNVKMALDIEIATYRKLLEGLKGTNESLERQMREMEE   393
                RE Q     K  +D  +     L+  LK     +  ++ E+E+
2-01031    168  RELQYFRTKKRRVDFRLEELETLIAKLKKKRRRVVTRLDEVEQ   210

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

Highlighted IDENTICAL residue ARG  381  index1  351  path  168  %Seq 100.00
Highlighted IDENTICAL residue GLU  382  index1  352  path  169  %Seq 100.00
Highlighted IDENTICAL residue LEU  386  index1  356  path  174  %Seq 100.00
Highlighted IDENTICAL residue TYR  400  index1  370  path  188  %Seq 100.00
Highlighted IDENTICAL residue LEU  404  index1  374  path  192  %Seq 100.00
Highlighted IDENTICAL residue LYS  334  index1  378  path  196  %Seq 100.00
Highlighted IDENTICAL residue SER  339  index1  383  path  201  %Seq 100.00
Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01031_1gk4A0.pir.txt.1GK4.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01031_1gk4A0.pir.txt PIR amino_acid 1GK4.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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