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
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
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/At2g13440-1qo8A.pir.txt

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

Assigned types to 723 residues in Sequence 2-13440, 71 remain unknown
Assigned types to 456 residues in Sequence 1qo8A, 338 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 At2g13440-1qo8A.pir.txt into sequence alignment.

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

>1QO8.pdb  Made from 8468 ATOM records in 1QO8.pdb
TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKL
QFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSW
DDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVD
KAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDI
KLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPE
IIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGA
KSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASM
TDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKAS
DAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGM
KVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHT
MGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVF
GRIAGDNAAKHALDTPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCK
SCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDI
KPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNAS
LAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWF
IEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVD
RTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGA
VVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITAT
GDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDG
NRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLY
KGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQS
PYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGY
NRLGGNAIADTVVFGRIAGDNAAKHALD

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

Best alignment:
1QO8.pdb   114  AAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILV   149
                 A    T  V+VVGAG AG  A+LA+ + GA+ +L+
2-13440     66  GATSDSTYDVIVVGAGHAGCEAALASARLGASTLLL   101

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

Highlighted IDENTICAL residue ALA  116  index1  115  path   67  %Seq 100.00
Highlighted IDENTICAL residue THR  121  index1  120  path   72  %Seq 100.00
Highlighted IDENTICAL residue VAL  124  index1  123  path   75  %Seq 100.00
Highlighted IDENTICAL residue VAL  126  index1  125  path   77  %Seq 100.00
Highlighted IDENTICAL residue VAL  127  index1  126  path   78  %Seq 100.00
Highlighted IDENTICAL residue GLY  128  index1  127  path   79  %Seq 100.00
Highlighted IDENTICAL residue ALA  129  index1  128  path   80  %Seq 100.00
Highlighted IDENTICAL residue GLY  130  index1  129  path   81  %Seq 100.00
Highlighted IDENTICAL residue ALA  132  index1  131  path   83  %Seq 100.00
Highlighted IDENTICAL residue GLY  133  index1  132  path   84  %Seq 100.00
Highlighted IDENTICAL residue ALA  136  index1  135  path   87  %Seq 100.00
Highlighted IDENTICAL residue LEU  138  index1  137  path   89  %Seq 100.00
Highlighted IDENTICAL residue ALA  139  index1  138  path   90  %Seq 100.00
Highlighted IDENTICAL residue GLY  144  index1  143  path   95  %Seq 100.00
Highlighted IDENTICAL residue ALA  145  index1  144  path   96  %Seq 100.00
Highlighted IDENTICAL residue LEU  149  index1  148  path  100  %Seq 100.00
Highlighted 16 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13440-1qo8A.pir.txt.1QO8.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13440-1qo8A.pir.txt PIR amino_acid 1QO8.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.