Hi Elaine, thank you for the hint! I believe that is what I needed! Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 19.12.2017 um 18:09 schrieb Elaine Meng:
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter