&&&&&&&&&&&&&&&&&&&& 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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