[phenixbb] Fw: bond deviation deected by Coot

Jeff Headd jjheadd at lbl.gov
Mon Dec 5 11:07:33 PST 2011


Hi Dialing,

How are you adding the hydrogens? Are they added following refinement,
or before refinement?

There are various Hydrogen bond length definitions used by different
programs, and that could explain the difference. What is the magnitude
of the deviation?

Jeff

On Mon, Dec 5, 2011 at 6:48 AM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> Dear All,
>
> Interestingly, most of the bonds deviation are from Asn! Btween ND2 and HD21
> or HD22.
>
> I am looking forward to getting an explanation from you.
>
> Cheers,
>
> Dialing
>
>
>
>
> ----- Forwarded Message -----
> From: Dialing Pretty <hdc123hdc123 at yahoo.com>
> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> Sent: Tuesday, 6 December 2011 12:44 AM
> Subject: bond deviation deected by Coot
>
> Dear All,
>
> After Pheneix refine, the quality of the structure improved significantly as
> analyzed by Molprobity. However the  bond deviation increased significantly
> after the refinement. Will you please tell me which refine function can be
> used to reduce the bond deviation detected by the Coot geometry analysis?
>
> Cheers,
>
> Dialing
>
>
>
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