-Just to make a note, there has actually been some discussion in the
published literature recently (ok maybe past ten years) about what
terms; simply steric (as originally) or hydrogen bonding etc
might be needed to explain observed backbone angular values.
Tommi
On Sep 26, 2011, at 5:44 PM
Dear Nat,
yes, I fully agree - all these restraints that improve the geometry
either by restraining to high-resolution structures or by introducing
H-bond restraints for secondary structures are very useful for
low-resolution structures!
I see your argument with the Ramachandran plot. But im
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa
wrote:
> when I played with H-bond restraints for secondary structures for the
> refinement of a 4.3 A structure (only a few weeks before they were
> introduced in phenix), I've made the following observation: at low
> resolution without H-bond restra
Dear Nat and other interested colleagues,
when I played with H-bond restraints for secondary structures for the
refinement of a 4.3 A structure (only a few weeks before they were
introduced in phenix), I've made the following observation: at low
resolution without H-bond restraints for seconda
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Dear Pete,
Coot offers using secondary structure restraints, i.e. this does not
refer to refinement but to model building where your calculations do not
apply.
It helps a great deal if you are looking at a patch of density at, say,
3.5A resolution wh
On Thu, Sep 22, 2011 at 4:18 PM, Pete Meyer wrote:
> In short, the effective observation to parameter ratio improves by ~4%.
> This seems like a relatively small improvement, especially if the trade-off
> is that Ramachandran statistics can't be used for validation anymore. It
> also seems like
aculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp
Original message
>Date: Thu, 22 Sep 2011 13:29:54 -0700
>From: CCP4 bulletin board (on behalf of Pavel Afonine
>)
>Subject: Re: [ccp4bb] question regarding secondary-structure restraints
>To: CCP4BB@JISC
Hi Pete,
the rationale is: at that low resolution the density map and traditional set
of restraints are not enough to preserve secondary structure elements during
refinement. For example, if you start with a model having good secondary
structure elements, they will be distorted after refinement ag
I've noticed that people seem to be using or recommending secondary
structure restraints for low resolution refinement lately, but I'm
somewhat confused about the logic underlying their use.
Using ballpark figures from a system I'm familiar with: 3 atoms
(9 positional parameters), 4500
