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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13720-1bgw_.pir.txt

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

Assigned types to 223 residues in Sequence 2-13720, 4 remain unknown
Assigned types to 203 residues in Sequence 1bgw_, 24 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 58  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 109  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 126  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 127  All residues are positively and negatively charged

Translated sequence file At2g13720-1bgw_.pir.txt into sequence alignment.

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

Error in function WYRM_assign_PDB_Atom_type()
Unable to assign atom H in residue PRO 1072

>1BGW.pdb  Made from 6832 ATOM records in 1BGW.pdb
RKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDY
YGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRY
GHLMIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSI
TKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFS
NLDRHLKIFHSLQGLFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKS
ELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAF
GTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEW
YLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHP
WFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLL
LGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLI
SPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQ
WEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPY
YGSPNDEIAEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLL
KLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

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

Best alignment:
1BGW.pdb   104  MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP   153
                MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP
1bgw_        1  MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP    50

1BGW.pdb   154  TKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLD   203
                TKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLD
1bgw_       51  XKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEXREYFSNLD   100

1BGW.pdb   204  RHLKIFHSLQ----------------------------------------   213
                RHLKIFHSLQ                                        
1bgw_      101  RHLKIFHSXXGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIP   150

1BGW.pdb   213  ---------GLFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV   254
                          LFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV
1bgw_      151  ISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV   200

1BGW.pdb   255  AQLAPYV   261
                AQLAPYV
1bgw_      201  AQLAPYV   207

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

Highlighted IDENTICAL residue GLY  532  index1  113  path   12  %Seq 100.00
Highlighted IDENTICAL residue SER  533  index1  114  path   13  %Seq 100.00
Highlighted IDENTICAL residue PHE  556  index1  137  path   41  %Seq 100.00
Highlighted IDENTICAL residue THR  562  index1  143  path   47  %Seq 100.00
Highlighted IDENTICAL residue PRO  563  index1  144  path   48  %Seq 100.00
Highlighted IDENTICAL residue LYS  566  index1  147  path   51  %Seq 100.00
Highlighted IDENTICAL residue VAL  567  index1  148  path   52  %Seq 100.00
Highlighted IDENTICAL residue SER  568  index1  149  path   53  %Seq 100.00
Highlighted IDENTICAL residue PHE  579  index1  160  path   64  %Seq 100.00
Highlighted IDENTICAL residue TRP  598  index1  179  path   93  %Seq 100.00
Highlighted IDENTICAL residue LYS  601  index1  182  path   96  %Seq 100.00
Highlighted IDENTICAL residue TYR  603  index1  184  path   98  %Seq 100.00
Highlighted IDENTICAL residue LYS  604  index1  185  path   99  %Seq 100.00
Highlighted IDENTICAL residue GLY  605  index1  186  path  100  %Seq 100.00
Highlighted IDENTICAL residue GLU  613  index1  194  path  108  %Seq 100.00
Highlighted IDENTICAL residue SER  619  index1  200  path  114  %Seq 100.00
Highlighted IDENTICAL residue ASN  620  index1  201  path  115  %Seq 100.00
Highlighted IDENTICAL residue ASP  622  index1  203  path  117  %Seq 100.00
Highlighted IDENTICAL residue PHE  628  index1  209  path  123  %Seq 100.00
Highlighted IDENTICAL residue LEU  683  index1  215  path  178  %Seq 100.00
Highlighted IDENTICAL residue ASN  689  index1  221  path  184  %Seq 100.00
Highlighted IDENTICAL residue ARG  691  index1  223  path  186  %Seq 100.00
Highlighted IDENTICAL residue ASN  695  index1  227  path  190  %Seq 100.00
Highlighted IDENTICAL residue LYS  701  index1  233  path  199  %Seq 100.00
Highlighted IDENTICAL residue LYS  706  index1  238  path  204  %Seq 100.00
Highlighted IDENTICAL residue LYS  713  index1  245  path  211  %Seq 100.00
Highlighted IDENTICAL residue LYS  714  index1  246  path  212  %Seq 100.00
Highlighted IDENTICAL residue LYS  717  index1  249  path  215  %Seq 100.00
Highlighted 28 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13720-1bgw_.pir.txt.1BGW.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13720-1bgw_.pir.txt PIR amino_acid 1BGW.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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