Hi Tim,
Yeah, riding hydrogens have always been on. I guess I need some more
investigation.
Chris
On Mon, 2012-05-07 at 15:36 +0200, Tim Gruene wrote:
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> Hi Chris,
>
> If the absence/ presence of hydrogens in the coordinate file made a
> difference in the refinement, I guess some parameter setting for the
> refinement program is awkward. Did you refine with riding hydrogens in
> both cases? Hydrogens can and should be added in riding positions even
> at low resolution, since they do not add to the number of parameters
> but help with anti-bumping restraints.
>
> Tim
>
> On 05/07/12 15:07, Christopher Browning wrote:
> > Hi,
> >
> > I've generally used PRODRG to create paramater files for any
> > ligands I add during refinement with CCP4 and/or PHENIX. I've been
> > trying READYSET from PHENIX as it greatly helps refining some metal
> > ion positions. But when I use READYSET, any ligand I add (in this
> > case EDO or ethylene glycol) gets modified to contain hydrogens. My
> > resolution is 2.5, definitely not high enough to resolve the
> > hydrogens, so why are they added. Should I just leave them there? I
> > have the same problem with another structure which has bizarre
> > sugar molecules so they are not standard COOT/CCP4/PHENIX small
> > molecules.
> >
> > As a test, I removed the hydrogens added to the ligands and the
> > refined protein coordinates are way different than when the
> > hydrogens are left in?
> >
> >
> > Cheers,
> >
> > Chris
> >
> >
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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--
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Switzerland
Tel: 0041 (0) 02 16 93 04 40
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