How to visualize a crystal from a unit cell PDB and how to draw the unit cell's axes? [closed]








**Closed**. This question needs [details or clarity](/help/closed-questions). It is not currently accepting answers.
 
 






---








**Want to improve this question?** Add details and clarify the problem by [editing this post](/posts/87349/edit).




Closed 5 years ago.








[Improve this question](/posts/87349/edit) 



I am looking at the following [PDB](http://www.rcsb.org/pdb/explore.do?structureId=3SOA) 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](http://www.rcsb.org/pdb/explore.do?structureId=3SOA)?
2. How can I build a crystal with 16 or so structures like this?


How can I build the [biological structure](https://cdn.rcsb.org/images/rutgers/so/3soa/3soa.pdb1-500.jpg) from asymmetric [unit cell](https://cdn.rcsb.org/images/rutgers/so/3soa/3soa.pdb-500.jpg)?


[![enter image description here](https://i.stack.imgur.com/ryUMs.png)](https://i.stack.imgur.com/ryUMs.png)




To view the $120^\circ$ angle, use any [molecular viewer](https://www.rcsb.org/pdb/static.do?p=software/software_links/molecular_graphics.html); one of the simplest and versatile desktop app is probably [Jmol](http://jmol.sourceforge.net/) (available on Windows, Linux, MacOS). [Download the PDB file](https://files.rcsb.org/download/3SOA.pdb), open it with the program. What you are going to see is the [asymmetric unit](http://reference.iucr.org/dictionary/Asymmetric_unit):


[![enter image description here](https://i.stack.imgur.com/SGfY2.png)](https://i.stack.imgur.com/SGfY2.png)


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](https://chemapps.stolaf.edu/jmol/docs/):



> 
> `{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](https://i.stack.imgur.com/lrYlv.png)](https://i.stack.imgur.com/lrYlv.png)


Finally, select `Style > Scheme > Cartoon`:


[![enter image description here](https://i.stack.imgur.com/9fhlh.png)](https://i.stack.imgur.com/9fhlh.png)


 3