Contouring ED Map: Sigma versus Chimera thresholds
Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely.
Thanks
Veer Sandeep Bhatt
Hi Veer, This previous reply may be useful:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 27, 2010, at 4:12 PM, Veer Bhatt wrote:
Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely. Thanks Veer Sandeep Bhatt
Hi,
Also regarding contouring ED maps: we have ccp4 maps that are fine in coot, but as soon as you display them in chimera they are sharply chopped in one direction, as if there is any problem with a border. Any suggestion, the effect it's particularly bad for a surface representation, but it's also obvious when you display it as a mesh.
Thank you!
Hector Viadiu viadiu@ucsd.edu
On Jan 27, 2010, at 4:12 PM, Veer Bhatt wrote:
Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely.
Thanks
Veer Sandeep Bhatt
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Hi Hector,
Not sure what "sharply chopped" means without a picture. But we have seen a problem where the map surface looks like sliced bread. It is caused by a bug in old Mesa OpenGL (3-d graphics) libraries on Linux, and is not a Chimera bug. The solution is to install a graphics driver which will also give you much faster rendering. Or you can disable Vertex Buffer Objects in the Chimera Debug Graphics Driver tool.
http://plato.cgl.ucsf.edu/trac/chimera/ticket/7201
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html
If this is not your problem you can submit a bug report with Chimera menu entry Help / Report a Bug and attach an image.
Tom
Hi,
Also regarding contouring ED maps: we have ccp4 maps that are fine in coot, but as soon as you display them in chimera they are sharply chopped in one direction, as if there is any problem with a border. Any suggestion, the effect it's particularly bad for a surface representation, but it's also obvious when you display it as a mesh.
Thank you!
Hector Viadiu
participants (4)
-
Elaine Meng -
Hector Viadiu -
Tom Goddard -
Veer Bhatt