[phenixbb] scaling in Fo-Fo maps

Pavel Afonine pafonine at lbl.gov
Thu Feb 4 09:59:19 PST 2016

Hi Smith,

> In line with the question of Xun, will you please introduce a way to 
> scale-up the intensity of cryo-EM to the level of intensity of x-ray 
> crystallography?

map comparison does not care where maps come from. You give it two maps 
on the same gridding (same gridding is essential, obviously) and it 
tells you pairs of contouring levels that will show equivalent 
representations of your maps.

> I have a read a paper, in which the author have done the 
> above-mentioned scaling-up in order to use the phenix reciprocal space 
>  refine for cryo-EM data refine,

Normally, you should not use reciprocal spare refinement when working 
with cryo-EM maps as your data, cryo-EM map, is in real space. And if 
you use real-space refinement it does not matter on what scale the input 
map is as it rescales it internally anyway.

> Currently with the availability of pheinix.real_space_refine, in a lot 
> of situations reciprocal refine for cryo-EM data is still necessary.

I would be interesting to hear about those cases!


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160204/47a86755/attachment.htm>

More information about the phenixbb mailing list