Bad automatic contouring

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-07-27)
Description
Automatic map contouring seems to be failing on some maps. This is the second one I've opened today where it's defaulted to a slightly negative contour (displaying as a solid cube). Doesn't appear to be anything wrong with the map itself... box is on the large side relative to the size of the positive density region.

Log:
UCSF ChimeraX version: 0.91 (2019-07-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4776 fromDatabase emdb

Opened emd_4776.map, grid size 256,256,256, pixel 1.08, shown at level
-5.08e-06, step 1, values float32  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Fixed.

ChimeraX sets the initial surface contour level when showing a map to enclose 1% of the grid points. I did not see that in the documentation but it should be added to the docs. It doesn't do an exact calculation of this level, instead it uses a histogram of data values. I've made it use an upper estimate of the 1% data value.

With this change map EMDB 4776 does not show a cube surface, but the initial level is too low. This is because the map has an excessively large box which is almost 99% zero values. It is hard to make a heuristic for initial contour level because of the diverse types of image data ChimeraX is used for (often 0 is not a base value, offsets are arbitrary, some maps fill entire box, others almost none of it).