How to get boundary conditions inluding triclicinc values

[alec...@gmail.com]

Hello, I have a triclinic file from LAMMPS that I am converting into a pdb file. Where do the alpha, beta, and gamma angles go in the below boundary conditions:

This is from an example on the FULLRMC cite

REMARK Boundary Conditions: 54.0 0.0 0.0 0.0 54.0 0.0 0.0 0.0 54.0 

Thank you,

Alec

[bachi...@e-aoun.com]

Hi Alec,

fullrmc naturally takes a,b and c vectors [[54.0, 0.0, 0.0], [0.0, 54.0 ,0.0], [0.0 ,0.0, 54.0 ]] instead of a,b,c modules and alpha, beta and gamma angles. 

The obvious reason behind this choice is that there is not guarantee that alpha beta and gamma are in the right order.

Now, if you can guarantee the following:

• alpha : Angle between b and c in degrees
• beta : Angle between c and a in degrees.
• gamma: Angle between a and b in degrees.

then you can use the following  code to do what you need

from pdbparser.BoundaryConditions import PeriodicBoundaries

BC = PeriodicBoundaries(params=None)

BC.set_vectors_using_abc_alpha_beta_gamma(a,b,c,alpha,beta,gamma)

vectors = BC.get_vectors()

I hope this helps

Bachir