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At2g01220.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01220-1_1nup_A.pir.txt

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

Assigned types to 387 residues in Sequence 2-01220-1, 41 remain unknown
Assigned types to 173 residues in Sequence 1nup_A, 255 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 246  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 247  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 248  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 249  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 280  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 281  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 282  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 283  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 284  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 285  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 286  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 287  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 288  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 289  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 308  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 309  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 310  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 311  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 312  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 313  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 314  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 315  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 316  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 317  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 318  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 319  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 320  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 321  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 322  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 323  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 324  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 325  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 326  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 327  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 328  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 329  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 330  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 331  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 332  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 333  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 334  All residues are positively and negatively charged

Translated sequence file At2g01220-1_1nup_A.pir.txt into sequence alignment.

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

>1NUP.pdb  Made from 3405 ATOM records in 1NUP.pdb
SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDT
YGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQWMETVKVLRHHHS
KLLAVPELKLLCGADVLKTFQTPNLWKDAHIQEIVEKFGLVCVGRVSHDP
KGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRALGQGQSVKYLIPDA
VITYIKDHGLYTKSRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMY
QVIQGIISPVNDTYGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQ
WMETVKVLRHHHSKLLRVPELKLLCGADVLKTFQTPNLWKDAHIQEIVEK
FGLVCVGRVSHDPKGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRAL
GQGQSVKYLIPDAVITYIKDHGLYT

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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 101  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 102  All residues are positively and negatively charged

Best alignment:
1NUP.pdb      7  LLACGSFNPITNMHLRMFEVA    27
                 ++  GSFNP+   HL++ EVA
2-01220-1   215  IILPGSFNPLHEGHLKLLEVA   235

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

Highlighted IDENTICAL residue GLY   13  index1   11  path  219  %Seq 100.00
Highlighted IDENTICAL residue SER   14  index1   12  path  220  %Seq 100.00
Highlighted IDENTICAL residue PHE   15  index1   13  path  221  %Seq 100.00
Highlighted IDENTICAL residue ASN   16  index1   14  path  222  %Seq 100.00
Highlighted IDENTICAL residue PRO   17  index1   15  path  223  %Seq 100.00
Highlighted IDENTICAL residue HIS   22  index1   20  path  228  %Seq 100.00
Highlighted IDENTICAL residue LEU   23  index1   21  path  229  %Seq 100.00
Highlighted IDENTICAL residue GLU   27  index1   25  path  233  %Seq 100.00
Highlighted IDENTICAL residue VAL   28  index1   26  path  234  %Seq 100.00
Highlighted IDENTICAL residue ALA   29  index1   27  path  235  %Seq 100.00
Highlighted 10 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01220-1_1nup_A.pir.txt.1NUP.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01220-1_1nup_A.pir.txt PIR amino_acid 1NUP.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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