Hi all, 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? Kind Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty [email protected] Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia
On Wed, Mar 21, 2012 at 1:48 AM, Christopher Wanty
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
Yes, it is a bug and I am working on the fix. Pavel On 3/21/12 7:32 AM, Nathaniel Echols wrote:
On Wed, Mar 21, 2012 at 1:48 AM, Christopher Wanty
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
participants (3)
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Christopher Wanty
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Nathaniel Echols
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Pavel Afonine