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
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Sequence 1
Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01390_1w3b_A.pir.txt

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

Assigned types to 577 residues in Sequence 2-01390, 4 remain unknown
Assigned types to 383 residues in Sequence 1w3b_A, 198 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 296  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 297  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 488  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 526  All residues are positively and negatively charged

Translated sequence file At2g01390_1w3b_A.pir.txt into sequence alignment.

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

>1W3B.pdb  Made from 5568 ATOM records in 1W3B.pdb
GPMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLD
RSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDF
IDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGR
LEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP
NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQ
GLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL
CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQ
QQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDGPMELAHREYQA
GDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQ
NPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALV
AAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAI
ETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNV
LKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRR
AIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSYRKAL
EVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNT
LKEMQD

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

Best alignment:
1W3B.pdb    69  AYSNLGNVYKERGQLQEAIEHYRHALRLKPDFID--GYINLAAALVAAGD   116
                 Y+ + +++ E G++Q     + H ++ K   ID   Y +L   + ++GD
2-01390    124  TYTTMLDIFGEAGRIQSMYSVF-HLMKEKGVLIDTVTYTSLIHWVSSSGD   172

1W3B.pdb   117  MEGAVQAYVSALQYNPDLYCVR-SDLGNLLKALGRLEEAKACYLKAIETQ   165
                ++GA++ +        +   V  +    +L A GR+EEA   Y + + ++
2-01390    173  VDGAMRLWEEMRDNGCEPTVVSYTAYMKMLFADGRVEEATEVYKEMLRSR   222

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

Highlighted IDENTICAL residue ALA   81  index1   69  path  124  %Seq  50.00
Highlighted IDENTICAL residue ARG   92  index1   80  path  135  %Seq 100.00
Highlighted IDENTICAL residue GLY   93  index1   81  path  136  %Seq 100.00
Highlighted IDENTICAL residue ASP  111  index1   99  path  153  %Seq  50.00
Highlighted IDENTICAL residue LEU  119  index1  107  path  163  %Seq 100.00
Highlighted IDENTICAL residue GLU  130  index1  118  path  174  %Seq 100.00
Highlighted IDENTICAL residue PRO  144  index1  132  path  188  %Seq  50.00
Highlighted IDENTICAL residue GLY  161  index1  149  path  206  %Seq 100.00
Highlighted IDENTICAL residue GLU  165  index1  153  path  210  %Seq 100.00
Highlighted IDENTICAL residue ALA  166  index1  154  path  211  %Seq 100.00
Highlighted IDENTICAL residue ALA  168  index1  156  path  213  %Seq 100.00
Highlighted IDENTICAL residue TYR  170  index1  158  path  215  %Seq 100.00
Highlighted IDENTICAL residue ILE  174  index1  162  path  219  %Seq 100.00
Highlighted IDENTICAL residue GLU  175  index1  163  path  220  %Seq 100.00
Highlighted 14 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01390_1w3b_A.pir.txt.1W3B.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01390_1w3b_A.pir.txt PIR amino_acid 1W3B.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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