Re: [ccp4bb] torsion restraints COOT

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Subject: torsion restraints COOT
From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-02-27

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From: "R {- dot -} M {- dot -} Garavito" garavito {- at -} MSU {- dot -} EDU
Date: 2008-02-27

Subject: Re: torsion restraints COOT
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-27

Hi Brenda,

Brenda Patterson wrote:
> I am doing molecular replacement with a model of sequence identity 42%.

If you used a CCP4 automated MR tool to generate your model, then the
"[Post MR] Fill Partial Residues" can conveniently restore side-chains
that have been "Schwarzenbachered".

> Have
> been trying numerous combinations of weighting in refmac of CCP4. However the
> geometry of the model is not being maintained.

"Geometry" in the sense of things that are restrainted or those that are
not?

> I am then trying manual fitting
> of the model in COOT. However when torsion restraints are applied in the
> refine/regularisation option the model comes out of the density.

Regularize and Real Space Refinement (RSR) are not the quite the same
thing.

> how would you tackle this please?

If, when using the RSR, you think that not enough emphasis is being
placed on the map, then you can change the weight (Set Matrix).

> i also have developed CIS peptides in places and have found
> that trying to revert these to trans is again causing the model to come out of
> the density severely.

Oh dear. Olden Coot?

There is a trick for even the wary, Refmac will add a CISPEP card to
its output where there are unlabelled CISPEPs (from
the output of Coot). If there are labelled CISPEPs (but not actually in
the structure) Refmac will make the peptide CISPEP.
Coot and Refmac are out of step (Coot is behind, it should catch up at
some stage). Currently you would have to hand-edit
the output of Coot/input to refmac to remove CISPEP cards that are
inappropriate.

> Does anyone think it's ok not to use the torsion
> restraints in COOT

Yes, I do. Torsion restraints are not (yet) applied across peptide
linkages.

> and simply use real space refine/regularisation as it is in
> COOT?
>

As long as your traffic lights are green[1], you should be OK.

[1]
http://www.ysbl.york.ac.uk/~emsley/coot/screenshots/traffic-lights-example.png

Paul.

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CCP4bb <-- 2008 <-- February 2008 <-- 27 February 2008

Previous message:
Subject: torsion restraints COOT
From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-02-27