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/At2g03420-1d0cA.pir.txt

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

Assigned types to 170 residues in Sequence 2-03420, 19 remain unknown
Assigned types to 129 residues in Sequence 1d0cA, 60 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 At2g03420-1d0cA.pir.txt into sequence alignment.

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

>1D0C.pdb  Made from 6595 ATOM records in 1D0C.pdb
GPKFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTRPS
PGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYH
LRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCSSAQEMFTYICNH
IKYATNRGNLRSAITVFPQRAPGRGDFRIWNSQLVRYAGYRQQDGSVRGD
PANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEAPELFVLPPELVLEVP
LEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEFSAAPFSGWYMSTEIGT
RNLCDPHRYNILEDVAVCMDLDTRTTSSLWKDKAAVEINLAVLHSFQLAK
VTIVDHHAATVSFMKHLDNEQKARGGCPADWAWIVPPISGSLTPVFHQEM
VNYILSPAFRYQPDPWKFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCL
GSLVLPRKLQTRPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERL
QEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARD
CSSAQEMFTYICNHIKYATNRGNLRSAITVFPQRAPGRGDFRIWNSQLVR
YAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEAP
ELFVLPPELVLEVPLEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEFSA
APFSGWYMSTEIGTRNLCDPHRYNILEDVAVCMDLDTRTTSSLWKDKAAV
EINLAVLHSFQLAKVTIVDHHAATVSFMKHLDNEQKARGGCPADWAWIVP
PISGSLTPVFHQEMVNYILSPAFRYQPDPW

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

Best alignment:
1D0C.pdb     1  GPKFPRVK     8
                GP+ P+++
2-03420     79  GPELPKIE    86

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

Highlighted IDENTICAL residue PRO   71  index1    5  path   86  %Seq 100.00
Highlighted 1 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03420-1d0cA.pir.txt.1D0C.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03420-1d0cA.pir.txt PIR amino_acid 1D0C.pdb A 100.0 BLOSUM62.dat 

completed successfully.

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

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