Hi Mischa,
We have a similar case. There is difference density, but only for some of
> the hydrogens (mostly methyl groups on Leu, Ile, Val, Ala). How does one
> decide which hydrogens to include in explicit refinement? The case in
> question has 0.99Å data (diffraction is significantly better, b
I have rarely worked with such data, but when we did, we always kept to
the riding hydroge positions in for refinement. You can check the
important ones by calculating sfs without them and seeing how well they
fit the map. For important residues like ASPS in catalytic triads that
can be very re
We have a similar case. There is difference density, but only for some of the
hydrogens (mostly methyl groups on Leu, Ile, Val, Ala). How does one decide
which hydrogens to include in explicit refinement? The case in question has
0.99Å data (diffraction is significantly better, but data were col
Can you see the hydrogens in the maps when they are excluded from the
phasing? There is little hope of refining them independently if you cant
see discrete peaks for them.
Eleanor
On 11/23/2010 05:18 AM, Kenneth Satyshur wrote:
Sirs:
We are attempting to refine hydrogens on a ligand (which
Even with SHELX, at 1.2A you should use a riding model for hydrogens and
not refine them freely. SHELX has a useful facility (OMIT $H or OMIT
followed by specific hydrogen atom names) to keep the hydrogen atoms in
the atom list but not include their contributions to the structure
factors. Then yo
Hi Kenneth,
...1.2A resolution... refinement of individual parameters for a hydrogen
atom... Hm.. Are you refining against neutron diffraction data?
Anyways, to answer your question: technically yes, you can refine individual
parameters of any selected atom(s) against X-ray or neutron data (or bo
Not sure if all the sirs will concur (and it might be a good idea to ask
madams also), but the answer is probably no. As far as protonation
state goes (guess that is what you are after, not oxidation), a better
strategy may be to look into the bond lengths between the appropriate
heavy atoms that
Sirs:
We are attempting to refine hydrogens on a ligand (which is 100 % occupied) and
has ~ 40 heavy atoms (CNO). The data is 1.2 A, 325 AA, 83335 data points in C2.
We have refined aniso and with H riding along (Rf= 17, R = 15) in CCP4. Can we
individually
refine the protons on the ligand? Let t
