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Measurements overview

Some tips & examples for doing measurements in #molstar at

  • label, distance, angle, dihedral
  • orientation (box/axes from principal components)
  • plane (best fit)

basic-final distance-top orientation-final plane-final

Basic measurements

  • Load PDB 1TQN; hide Polymer and Water component
  • Enable selection mode; set granularity to "Atom/Element"
  • Open Measurements panel & select some atoms
  • Click one of the options available (depend on number of selected atoms)


basic-start basic-select

Distance example

We compare closed (PDB 6VXX) and open (PDB 6VYB) state of SARS-CoV-2 spike glycoprotein

  • Superpose both states
  • Select Leu 511 from chain B in both states
  • Add "distance" & "label" using Measurements panel
  • Adjust visual options


distance-select label-adjust distance-side

Orientation box/axes

We use "orientation" ellipsoids to show the 3 domains of Pyruvate Kinase (PDB 1PKN)

  • Select the PK domain (116-217)
  • Add "orientation" and "label"; adjust visual options
  • Repeat for PK N (12-115 & 218-395) and PK C (396-530)


orientation-adjust orientation-simplified

Best fit plane

We can add two best fit planes indicating lipid membranes to the bacterial flagellar motor-hook complex (@Jiaxing_Tan_ et al.)

  • Select a few residues at the edge of the M-ring protein
  • Add "plane" using Measurements panel
  • Adjust visual options
  • Repeat for the L-ring protein


plane-select plane-adjust