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Tangram Examples (Examtangrams?)

QMSetup

Open any molecule and click Preview.

Dummy Atoms

  1. In Chimera Command Line: open 1F8N.
  2. Select duplicated HIS atoms nearby metal center and delete them with del sel.
  3. Select Geometry=Octahedron
  4. Click Run.

NCIPlot

  1. In Chimera Command Line: open 1VRH.
  2. In Chimera Command Line: sel :SD8 < 5
  3. Switch to Selection tab and click Run. (It will take around 2 minutes).

NormalModes

  1. In Chimera Command Line: open 1ZE9.
  2. Select ProDy.
  3. Delete all but first NMR model: del ~#0.1.
  4. Click Run.

PLIP

Open 3pk2 and click Run.

PoPMuSiC

  1. open 1RFO
  2. del ~#0.1
  3. Choose POP/POPS files from ~/.local/insilichem/tangram/popmusicgui/examples

PropKa

Open 1YFU and click Run.