[phenixbb] Hydrogens

Pavel Afonine pafonine at lbl.gov
Wed Mar 21 07:50:49 PDT 2012

Yes, it is a bug and I am working on the fix.

On 3/21/12 7:32 AM, Nathaniel Echols wrote:
> On Wed, Mar 21, 2012 at 1:48 AM, Christopher Wanty
> <christopher.wanty at uwa.edu.au>  wrote:
>> I’ve been refining with riding hydrogens, and from what I’ve read hydrogen
>> contribution should be included in Fo calculation automatically for maps.
>> What I’m seeing after refinement is a lot of little bits of green in the
>> difference density that look like they could be explained by hydrogens. I’m
>> working at 1.4A, attached image gives an example and  shows contours at 3
>> sigma for difference map.
>> Is there a setting/parameter I need to adjust to get this to work properly?
> It's a bug:
> http://www.phenix-online.org/pipermail/phenixbb/2012-March/018460.html
> -Nat

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