[phenixbb] Fwd: Hi Res Model. Maybe its time to Include Hydrogens?

[Pavel Afonine]

Yuri,

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"
http://phenix-online.org/newsletter/

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 
going on.

Thanks,
Pavel

On 3/1/12 6:57 PM, Yuri wrote:
>
> Sue:
> I am not sure they are being included... I have the option checked, 
> but the R values and difference maps tell me otherwise
> Pavel:
> 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.