Dear Ed,
no, if you start with model that has no hydrogens, they will not be
generated internally.
Pavel.
On 9/15/10 2:58 PM, Ed Pozharski wrote:
Sure. But if I start with model that has no hydrogens, they will be
generated but not passed to the output, right. just like refmac.
On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
Dear Ed,
On 9/15/10 2:47 PM, Ed Pozharski wrote:
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
So the riding hydrogen model is imperfect. At least with
phenix.refine
you can measure it, unlike the default behavior of REFMAC. (But you
can
tell it to write hydrogens out, I believe).
My impression is that default behavior of phenix.refine is the same - I
had to change parameters to include hydrogens in the output.
No, if your input file contains H atoms, the output file will contain
them too (in phenix.refine). You don't have to change any parameters for
this.
Pavel.
