revised 3/01/05, 1:00am
Pymol Scripts and Coordinates for Space Group Visualization
* Something is wrong with P222.
Assignment 1. What is the 3x3 matrix for a 4-fold rotation around a line along the x-axis?
What is the 3x3 matrix for a 4-fold rotation around a line along the y-axis?
Assignment 2. Modify one of the scripts and one of the coordinate files
so that in combination they make a reasonable crystal (for space groups other than P1 and P2. Do this twice (i.e., do two
different space groups). It is important that atoms do not overlap, which can be seen
using the sphere representation. And it
is important that there are not huge cavities in the crystal.
You must set the cell axis and the molecule position to make it right.
You can work together. But I would like
each of you to produce two different space group/unit cells. Please comment the files; put your name in
both the script and the coordinate file. I plan to post your results.
Please use the file naming scheme that I used above; p1_script.pml, p2_script.pml... and p1_coords.pdb, p2_coords.pdb... etc.
I have played a little with P61 and have made it work. I used angles of 90 90 240, which is not right. the angles should be 90 90 120.
Some possibilities are listed below. (I have not tried all of these)
You must follow some rules:
Orthoganol space group (P2, P222, etc); all angles must be 90, no restrictions on a,b,c
Tetragonal space group (P4, P422 etc); all angles 90, a=b
Hexagonal space group (P6, etc); alpha 90, beta 90, gamma 120, a=b
From the Pymol manual
The format of the CRYST1 record is as follows.
1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a a (Angstroms).
16 - 24 Real(9.3) b b (Angstroms).
25 - 33 Real(9.3) c c (Angstroms).
34 - 40 Real(7.2) alpha alpha (degrees).
41 - 47 Real(7.2) beta beta (degrees).
48 - 54 Real(7.2) gamma gamma (degrees).
56 - 66 LString sGroup Space group.
67 - 70 Integer z Z value. # ignored by PyMOL