Dear Phil & CCP4ers,
to my knowledge, none of the existing reciprocal-space refinement
programs is really suitable for low-resolution refinement. In my
opinion, what is clearly missing, are automatic hydrogen-bond-
restraints that would stabilize all secondary structures and other
structurally important H-bonds during refinement at low resolution.
The old X-Plor program had hydrogen bonds parametrized.
In real space refinement, this is also missing in Coot that screws up
structures at low resolution. I use Moloc in these cases, because it
accounts for all hydrogen bonds and does stable real space refinement
of proteins and nucleic acids at any low resolution.
I really hope, that also the chemical knowledge of the structurally
important hydrogen bonds gets incorporated both into reciprocal space
and real space refinement programs in the future, since more and more
biologically important structures are solved at medium to low
resolution!!!
Best regards,
Dirk.
Am 08.01.2009 um 18:09 schrieb Phil Evans:
> Does anyone have a good way of imposing secondary structure
> restraints in a low resolution refinement?
>
> I've done this in the past as hydrogen bond distance restraints
> within helices, input to refmac as "LINK"s , with the list generated
> with a little program and certain amount of pain
>
> refmac now accepts an explicit list of external restraints, as does
> phenix.refine, but I'm looking for a way of generating these lists
> for quite a large structure without too much hackery, perhaps from a
> hydrogen-bond or secondary structure assignment program. Helices are
> reasonably straightforward (I can see how to do them from eg DSSP),
> but sheets are more complicated.
>
> Any suggestions? I'm sure that someone must have done this
>
> Phil
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Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [log in to unmask]
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