Canavan Disease: Task 04 - Journal

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Revision as of 13:00, 7 August 2013 by Mahlich (talk | contribs)

Task 04 Working Log

data gathering

pymol

  • loaded sequneces with "fetch XXXX"
  • for 2I3C, 2O4H, 2Q51, 2GU2 and 2QJ8 there was a selection of only the chain A created (via "select XXXX_A, XXXX and chain A")
  • the alignment was done from the action menue -> align -> to selection -> 2I3C (alternatively via align XXXX, 2I3C_A however this results in slightly different RMSD most certainly due to the fact that the alignemnt via the action menu does some additional preselection)
  • updated to superimpose (super XXXX & alt A+, 2I3C_A & B+)
  • back ground set to white
  • zinc via selection tool selcted as sphere
  • all structures represented as cartoon
  • all structures colored with one color
  • 2I3C always orange
  • ray
  • save png with "png XXXX.png"
  • RMSDs:
    • 2O4H = 0.341
    • 2Q51 = 0.172
    • 2GU2 = 0.619
    • 2QJ8 = 7.001
  • Updated RMSD:
    • 2O4H = 0.445
    • 2Q51 = 0.223
    • 2GU2 = 0.493
    • 2QJ8 = 3.474

SSAP

  • used Web interface

LGA

  • used the web interface

CE

  • used the web interface by PDB (jCE)
  • stored only the overview

Topmatch

  • used web interface

Evaluation with structures

  • generation of models:
    • first get the sequences which are used to generate the model via: hhsearch -i 2I3C.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70currenthhm_db -o 2i3C.hhr -Z 10000 -B 10000
    • chosing the sequences based on seqId / Probability and evalue -> compared the resutls auf hhsearch to the rsults of psiblast from task 02 to get the "true sequence identity"
    • Table here:
    • genereate the models with: /usr/share/hhsuite/scripts/hhmakemodel.pl -i ~/mapra/2i3C.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 1 2 4 25 32 35 115 -ts ~/mapra/2I3C.pdb
    • all models are split into single files
    • hhsearch based on fasta sequence of 2I3C_A -> 2I3C.pdb split into only Chain A as well
    • lga runs vie webserver