All:
Following up on Carsten's comment. Buster also does not add hydrogen atoms automatically. It does have a command external to buster, hydrogenate, which uses the Duke University (read MolProbity) group's reduce underneath along with CIF restraint files for ligands to allow reduce to properly hydrogenate both protein and ligands. So Carsten's statement "one has to be very conscientious to add hydrogens back after mutating or adding residues" holds for buster as well.
Steven
P.S. I should note that Gelly, which is Buster's geometry engine, does an excellent job of producing typically >90th percentile Clash and MolProbity scores even in the absence of hydrogen atoms.
-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software [mailto:[log in to unmask]] On Behalf Of Schubert, Carsten [JRDUS]
Sent: Wednesday, May 27, 2015 12:54 PM
To: [log in to unmask]
Subject: Re: Dragged refinement fails with riding hydrogens
Hi Tim,
that does not work for phenix, not sure about Buster/TNT; refmac behavior is different. In phenix, which uses a riding model as well, but defines explicit hydrogens, one has to be very conscientious to add hydrogens back after mutating or adding residues. In part this is a phenix issue as well, but all in all I do have to side with Oliver on this one. Coot is not very well adapted to a handle explicit hydrogens and could benefit from improvement in that regard.
Cheers,
Carsten
-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software [mailto:[log in to unmask]] On Behalf Of Tim Gruene
Sent: Wednesday, May 27, 2015 12:16 PM
To: [log in to unmask]
Subject: Re: [COOT] Dragged refinement fails with riding hydrogens
Hi Oliver,
unless these are neutron data, you could simply remove the hydrogen atoms from the model before model building. They would be regenerated on the next round of refinement. At least this is the philosophy of some refinement programs.
Cheers,
Tim
On Wed, May 27, 2015 at 04:16:38PM +0100, Oliver Clarke wrote:
> Hi all, dragged refinement doesn't seem to work for structures with riding hydrogens - see linked screen recording showing dragged refinement of the same structure with and without hydrogens.
>
> https://www.dropbox.com/s/15xs8ylhrx98ljk/dragged_refinement_H_bug.mov
> ?dl=0
>
> Would it be possible to alter this behaviour at some point such that hydrogens remain firmly attached during dragging, to remedy this?
>
> In the past I have got around this by just doing real space corrections in the absence of any hydrogens and adding them back in before every cycle of reciprocal space refinement, but this does not seem like the optimal way to be doing things.
>
> Cheers,
> Oliver.
>
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
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