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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01180_2a96_A.pir.txt

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

Assigned types to 302 residues in Sequence 2-01180-1, 0 remain unknown
Assigned types to 161 residues in Sequence 2a96_A, 141 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

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

Translated sequence file At2g01180_2a96_A.pir.txt into sequence alignment.

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

>2A96.pdb  Made from 6960 ATOM records in 2A96.pdb
QPFHSPEESVNSQFYLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRWKQAA
EDADISVENIARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAK
KYYMRTRPFVLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQAR
PERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQ
KSLAKVREELNDKNNLLMQPFHSPEESVNSQFYLPPPPGNDDPAFRYDKE
AYFKGYAIKGSPRWKQAAEDADISVENIARIFSPVVGAKISPKDTPETWN
MLQNLLKVGGYYATASAKKYYMRTRPFVLFNHSTCRPEDENTLRKDGSYP
SGHTAYSTLLALVLSQARPERAQELARRGWEFGQSRVICGAHWQSDVDAG
RYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLSQPFHSPEESVNSQF
YLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRWKQAAEDADISVENIARIF
SPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPFVLFNH
STCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELARRGWEF
GQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKN
NLLMQPFHSPEESVNSQFYLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRW
KQAAEDADISVENIARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYAT
ASAKKYYMRTRPFVLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVL
SQARPERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTI
PAFQKSLAKVREELNDKNNLLS

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

Best alignment:
2A96.pdb   278  IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF   327
                IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF
2a96_A       1  IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF    50

2A96.pdb   328  VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR   377
                VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR
2a96_A      51  VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR   100

2A96.pdb   378  RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE   427
                RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE
2a96_A     101  RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE   150

2A96.pdb   428  LNDKNNLLSQ   437
                LNDKNNLLS+
2a96_A     151  LNDKNNLLSK   160

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

Highlighted IDENTICAL residue ILE   86  index1  281  path   81  %Seq 100.00
Highlighted IDENTICAL residue LYS   94  index1  289  path   89  %Seq 100.00
Highlighted IDENTICAL residue THR  119  index1  314  path  114  %Seq 100.00
Highlighted IDENTICAL residue SER  121  index1  316  path  116  %Seq 100.00
Highlighted IDENTICAL residue LYS  123  index1  318  path  118  %Seq 100.00
Highlighted IDENTICAL residue ARG  128  index1  323  path  123  %Seq 100.00
Highlighted IDENTICAL residue ARG  130  index1  325  path  125  %Seq 100.00
Highlighted IDENTICAL residue PRO  131  index1  326  path  126  %Seq 100.00
Highlighted IDENTICAL residue CYS  140  index1  335  path  148  %Seq 100.00
Highlighted IDENTICAL residue SER  153  index1  348  path  161  %Seq 100.00
Highlighted IDENTICAL residue PRO  155  index1  350  path  163  %Seq 100.00
Highlighted IDENTICAL residue SER  156  index1  351  path  164  %Seq 100.00
Highlighted IDENTICAL residue GLY  157  index1  352  path  165  %Seq 100.00
Highlighted IDENTICAL residue HIS  158  index1  353  path  166  %Seq 100.00
Highlighted IDENTICAL residue THR  159  index1  354  path  167  %Seq 100.00
Highlighted IDENTICAL residue SER  162  index1  357  path  170  %Seq 100.00
Highlighted IDENTICAL residue LEU  169  index1  364  path  177  %Seq 100.00
Highlighted IDENTICAL residue SER  170  index1  365  path  178  %Seq 100.00
Highlighted IDENTICAL residue GLY  188  index1  383  path  211  %Seq 100.00
Highlighted IDENTICAL residue SER  190  index1  385  path  213  %Seq 100.00
Highlighted IDENTICAL residue ARG  191  index1  386  path  214  %Seq 100.00
Highlighted IDENTICAL residue VAL  192  index1  387  path  215  %Seq 100.00
Highlighted IDENTICAL residue HIS  197  index1  392  path  220  %Seq 100.00
Highlighted IDENTICAL residue ASP  201  index1  396  path  224  %Seq 100.00
Highlighted IDENTICAL residue VAL  202  index1  397  path  225  %Seq 100.00
Highlighted IDENTICAL residue ALA  204  index1  399  path  227  %Seq 100.00
Highlighted IDENTICAL residue GLY  205  index1  400  path  228  %Seq 100.00
Highlighted IDENTICAL residue GLY  209  index1  404  path  232  %Seq 100.00
Highlighted IDENTICAL residue ALA  214  index1  409  path  237  %Seq 100.00
Highlighted 29 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01180_2a96_A.pir.txt.2A96.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01180_2a96_A.pir.txt PIR amino_acid 2A96.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.