&&&&&&&&&&&&&&&&&&&& 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
Got here 4
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
Got here 3
Got here 4
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/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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