3D Volume Viewer: large objects vanish into background

Hi CryoSPARC team,

The 3D volume view has a cutoff for zooming out (and shadowing issue as well). I realise this is a very specific scenario that this will occur in, but with CS4.4 I wanted to see how CS handles big things again…

The default parameters:

Change threshold to show (currently very low res) full object):

Zoom out a little:

A little more:

You can already see the shadow depth causing issues…

A little more:

Almost the full particle is visible…

A little more:

Whole particle can be seen, but it’s so dark it’s hard to see…

A little more:

This shows the particle disappearing into the background gridded blue.

Finally, the particle disappears:

For this low res (ab initio) example, obviously I’m not too worried about seeing anything (as at the target resolution there is nothing/little to see - this was an intermediate step, approx. 95Å) but I wasn’t expecting the dramatic shadow gradient, nor the background to just swallow the particle!

This ab initio is very heavily binned (more than I usually do in RELION for giant particles) so the box size is 280 pixels…

Can the shadowing be disabled somehow?

Thanks @rbs_sci for reporting and sending over your map for us to investigate. We have been able to reproduce the issue and are working on a fix.


1 Like

Thanks, @sdawood! :smiley: