Hmm - there are some hydrogens which are simply not fixable from
chemistry, or electron density at low (ie <1.5A!) resolution - any of us
who have looked in vain for them can testify to that - and I cant think
that it is good to add in scatterers when you dont know where they are.
The ones det
HI James,
Obviously, this depends a bit on which refinement program you use, and I am
> not familiar with all of them. However, I have had some conversations with
> Garib "refmac" Murshudov and Pavel "phenix.refine" Afonine about this, and
> the shocking answer appears to be "no".
>
wow, I've g
Thanks George! I didn't feel remotely qualified to describe how SHELX
works, and that is why I didn't.
On 1/7/2011 3:11 PM, George M. Sheldrick wrote:
Dear James,
I did once write a refinement program so I should try to answer your
question. All hydrogen atoms attached to C and N in standard
Dear James,
I did once write a refinement program so I should try to answer your
question. All hydrogen atoms attached to C and N in standard proteins and
almost all in DNSs and RNAs can be calculated geometrically with no
ambiguities. This has been standard practice in SHELX for about 35 years
On Fri, Jan 7, 2011 at 10:49 AM, James Holton wrote:
> But what about MolProbity? and all those neat inter-digitating hydrogens?
> Should it not be possible for the refinement program to be "smarter" about
> where it puts riding hydrogens? Well, that is always possible, but I don't
> think MolP
Obviously, this depends a bit on which refinement program you use, and I
am not familiar with all of them. However, I have had some
conversations with Garib "refmac" Murshudov and Pavel "phenix.refine"
Afonine about this, and the shocking answer appears to be "no". Carbon
has six electrons, e
Hi Kenneth,
There are recognized advantages to including riding hydrogens during
refinement, even at low resolution. Others have written on this better than I
could (the following link is a post to the CCP4bb from the archives):
http://www.ysbl.york.ac.uk/ccp4bb/2002/msg01215.html
-An
