 |
 |
Hi Anasuya, at least, Gerard Kleywegt's program "moleman2" from the Uppsala Software Factory <http://xray.bmc.uu.se/usf/> 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 > > -- ******************************************************* Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [log in to unmask] WWW: www.genzentrum.lmu.de *******************************************************