Initial map thresholds too low for 3kf2 with structure factors

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
The map thresholds after "open 3kf2 structureFactors true" seem too low.

Tristan says scrolling can adjust threshold levels, but this is on a Mac laptop with a trackpad and scrolling is not available (2-finger drag does rotation).  Volume Viewer is not shown  so that method of adjusting the thresholds is also not immediately available.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3k2f structureFactors true

Summary of feedback from opening 3k2f fetched from pdb  
---  
notes | 3k2f title:  
Nitric oxide-donating carbonic anhydrase inhibitors for the treatment of open-
angle glaucoma [more info...]  
  
  
  
  
  
| Chain information for 3k2f  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
1.3/A | Carbonic anhydrase 2  
  
  
  
  
  
  
Non-standard residues in 3k2f #1.3  
  
---  
  
  
  
  
HG — mercury (II) ion  
  
  
  
NKX — (2S)-2,3-bis(nitrooxy)propyl
ethyl[(4S,6S)-6-methyl-7,7-dioxido-2-sulfamoyl-5,6-dihydro-4H-thieno[2,3-b]thiopyran-4-yl]carbamate  
  
  
  
ZN — zinc ion  
  
  
  
  
Resolution: 1.9820224808309657  
  
  

> hide #!1.3 models

> show #!1.3 models

> hide #!1.1 models

> show #!1.1 models




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

More comments about this in ticket #2002.

[tic20@…]

Come to think of this, I already have some code for exactly this task which gets used when associating a cryo-EM map with a model in Clipper. In cryo-EM maps the rmsd isn’t particularly meaningful due to all the empty space, and absolute values are all over the place. So, I select the contour based on the fraction of the model’s van der Waals volume it will enclose. Should be straightforward to apply it to the crystallographic maps as well.
 

 

[Tristan Croll]

Loaded standard (i.e. 2FO-FC) maps will now auto-contour to reasonable levels (varied slightly depending on whether the map is sharpened or not - that is, the least-sharp map (displayed as a wireframe) is set to a lower contour than the rest). Difference maps (FO-FC) are still contoured at +/- 3 sigma - hard to see how to do better than this, since a difference map isn't *expected* to cover the model.