[PyMOL] Putting a protein molecule into a grid and traversing through the grid

From: Dirk Kostrewa
Date: 28 October 2011 13:29

Hi Anasuya,

at least, Gerard Kleywegt's program "moleman2" from the Uppsala Software Factory has a command "XYz ALign_inertia_axes" should do your first task.
From the moleman2 manual: "This will move the currently selected atoms such that their centre-of-gravity is at the origin (0,0,0); then it will calculate the three principal inertia axes, and align the selected atoms such that these axes coincide with the X, Y and Z axis. This alignment is done such that the major inertia axis coincides with the X-axis (largest eigenvalue), and the minor inertia axis coincides with the Z-axis (smallest eigenvalue)."

Best regards,

Dirk.

Am 27.10.11 14:17, schrieb Anasuya Dighe:

how do i put a protein molecule inside a cube with x-axis spanning till the largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis spanning till the largest z-coordinate?  Once i do this, can i divide the larger cube(i.e. the one holding the entire protein) into smaller ones of lesser dimensions? Say, 5A x 5A x 5A?  Once i generate these smaller cubes, is there a way via pymol, by which i can navigate through the protein molecule, (smaller)cube by (smaller)cube? As in, can pymol be used to tell me which residues are lying in which (smaller) cube and so on?  Can all this be done in a single pymol window/script? please let me know.  Thanks -Anasuya