I am looking at the following PDB experimental data:

Length (Å)  Angle (°)
a = 155.72  α = 90.00
b = 155.72  β = 90.00
c = 106.16  γ = 120.00

I find it hard to imagine in my head what does it mean to have $\gamma = 120.00$ as an angle.

  1. How can I see the unit cell's axes on the following structure?
  2. How can I build a crystal with 16 or so structures like this?

How can I build the biological structure from asymmetric unit cell?

enter image description here


To view the $120^\circ$ angle, use any molecular viewer; one of the simplest and versatile desktop app is probably Jmol (available on Windows, Linux, MacOS). Download the PDB file, open it with the program. What you are going to see is the asymmetric unit:

enter image description here

Now, right click and select Symmetry > Reload {444 666 1} + Display 555. This will basically populate the entire unit cell (might take a while). This command is described in interactive scripting documentation:

{ijk i'j'k' 1} Loads a block of unit cells within the range ijk and i'j'k' (which should include 555), normalizing the operators to move the geometric center of the generated set of atoms into cell 555, then applying the lattice translation.

enter image description here

Finally, select Style > Scheme > Cartoon:

enter image description here

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  • $\begingroup$ Can you elaborate on the parameters: Reload {444 666 1} + Display 555 $\endgroup$ – 0x90 Dec 17 '17 at 11:57
  • $\begingroup$ @ox90 Basically, it's a Jmol code for displaying the entire content of a unit cell, disregarding the molecular boundaries. $\endgroup$ – andselisk Dec 17 '17 at 12:04
  • $\begingroup$ @ox90 chemapps.stolaf.edu/jmol/docs $\endgroup$ – andselisk Dec 17 '17 at 12:37
  • $\begingroup$ I am trying to do the same thing with VMD, but I don't know how to do it. How do I take the asymmetric unit cell and rotate and shift it to create the total biological assembly . $\endgroup$ – 0x90 Dec 24 '17 at 9:36
  • $\begingroup$ @ox90 Sorry, I don't really use VMD. $\endgroup$ – andselisk Dec 24 '17 at 9:40

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