On Apr 18, 2024, at 1:09 AM, Luca Pellegrini <lp212@cam.ac.uk> wrote:

Hi Tom,

Thank you for the explanation. After flipping the map my outline boxes don’t align (see attached for original and flipped).

Best wishes,

Luca

<outlineBox.png>

On 17 Apr 2024, at 19:17, Tom Goddard <goddard@sonic.net> wrote:

Hi Luca,

 When ChimeraX flips a map it keeps the same origin grid index.  That means the box containing the flipped volume aligns exactly with the box of the original volume.  You can check this by showing the outline boxes of both volumes

volume showoutline true

 Maybe what you mean is you have a symmetric structure that you think is centered at the middle of the map box, so you expect that flipping it will keep the center in the same place, but instead you see it move.  That would be because your structure isn't actually centered in the middle of the map box.  One reason for that can be that the map has an even number of grid points, e.g. 256 and so no grid point lies at the center of the box -- the geometric center is half way between two grid points, and some reconstruction software likes to put the center at a grid point, off-center.

Tom

On Apr 17, 2024, at 3:50 AM, Luca Pellegrini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

if I flip a map with ‘volume flip #ID', save the flipped map and then open it, the saved copy is noticeably shifted by a small amount relative to the original flipped map. This doesn’t happen if I save and reopen the map without flipping. Can you please explain what causes this and if it can be avoided?

Thanks,
Luca  

Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
UK




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