[phenixbb] Fwd: Hi Res Model. Maybe its time to Include Hydrogens?
pafonine at lbl.gov
Thu Mar 1 19:19:56 PST 2012
scattering from H is always included when input PDB file has H atoms in
it (and it is a refinable parameter), regardless whether you use
"hydrogens.refine=individual" or "hydrogens.refine=riding". The only
(main) difference between the two options is that "riding" option does
not add extra individual refinable parameters arising from H atoms.
Again, more details are here and in references therein:
"On contribution of hydrogen atoms to X-ray scattering"
The bug I mentioned in my reply is that when "hydrogens.refine=riding"
is used the scattering from H is included everywhere but maps, so that
was explaining to me why you still see H atoms in residual map even
though you have them in your model. I will fix this bug as soon as I
can, but probably not in a next few days.
Now you are saying that you tried both options and that did not make any
difference map-wise. This is something I can't explain. Therefore, could
you please send me the model and data, and I will investigate what's
On 3/1/12 6:57 PM, Yuri wrote:
> I am not sure they are being included... I have the option checked,
> but the R values and difference maps tell me otherwise
> A bug? That would be consistent with the behavior I observe. Even when
> I enable refinement with hydrogens individual or riding, i see
> essentially no difference in maps or Rfree values.
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