Skip to content

Instantly share code, notes, and snippets.

View gp0's full-sized avatar

Simon gp0

5 followers · 10 following
  • Germany
View GitHub Profile
@gp0
gp0 / gist:4035fdac58a67f1fa669
Last active August 29, 2015 14:18
  • Wir suchen zuerst mit BLAST (lokal, NCBI, oder EBI) nach Sequenzen S_i (i=1,...,n) in der PDB (d.h. Sequenzen zu denen bekannte Strukturen gehören), die ähnlich sind zu S_0. [BLAST ist Gegenstand der nächsten Vorlesung]

NCBI implementiert.

Modul: WebBLAST (Simon/Henning)

  • Die besten Hits (E-value < threshold) alinieren wir mit MAFFT.
@gp0
gp0 / gist:a8e7d27edf979f8c0e0d
Created March 18, 2015 21:51
Kabsch test run
simon@t430 ~/.julia/v0.3/BiomolecularStructures $ julia src/PDB/pdb.jl
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 5037.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 5080.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 5124.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 5167.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 5211.