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/At2g10390-1g3jA.pir.txt

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

Assigned types to 194 residues in Sequence 2-10390, 11 remain unknown
Assigned types to 174 residues in Sequence 1g3jA, 31 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

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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 35  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 36  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 37  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 158  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 159  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 160  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 161  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 162  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 163  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 164  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 165  All residues are positively and negatively charged

Translated sequence file At2g10390-1g3jA.pir.txt into sequence alignment.

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

>1G3J.pdb  Made from 7531 ATOM records in 1G3J.pdb
HAVVNLINYQDDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEA
SRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFK
SGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMV
ALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTY
EKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLW
TLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYK
NKMMVCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQN
AVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAI
PRLVQLLVRAHQDTQRRFVEGVRMEEIVEGCTGALHILARDVHNRIVIRG
LNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTE
LLHSRNEGVATYAAAVLFRMSEPQLNSGGGDELGANDELIRFKDEGEQEE
DLADVKSSLVNESHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTL
HNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQ
ESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVE
AGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLL
GSDDINVVTCAAGILSNLTCNNYKNKMMVCQVGGIEALVRTVLRAGDRED
ITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKA
TVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGQQFVE
GVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQR
VAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRM
SEPQLNSGGGDELGANDELIRFKDEDLADVKSSLVN

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

Best alignment:
1G3J.pdb     1  HAVVNLINYQDDAELATRAIPE    22
                H++   IN Q   ++A   IPE
2-10390      9  HSITQPINTQ--RKIARLYIPE    28

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

Highlighted IDENTICAL residue HIS  134  index1    1  path    9  %Seq 100.00
Highlighted IDENTICAL residue LEU  148  index1   15  path   21  %Seq 100.00
Highlighted 2 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10390-1g3jA.pir.txt.1G3J.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10390-1g3jA.pir.txt PIR amino_acid 1G3J.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.