Refmac does an excellent job at low resolution. Many of the features available in version 5.6.x are described in a very recent Refmac paper
Murshudov et al. REFMAC5 for the refinement of macromolecular crystal structures.
Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 355-67
For example:
Jelly body restraints are controlled by
ridge distance sigma <value> # Default 0.1
ridge distance dmax <value> # Default 4.2
ridge atoms <sigma>
ridge bvalue <sigma>
keywords. You will find info on this under Harmonic distance restraints (Ridge regression)
External restraints (distance) are controlled by a syntax like that below:
exte dist first chain A residue 78 atom O second chain A residue 82 atom N value 3.000 sigma 0.05
More information at under External restraints. As Rob pointed out ProSMART can generate the above type of restraints for you.
Phenix can also provide a list of external distance restraints which can be interpreted by Refmac
phenix.secondary_structure_restraints model.pdb format=refmac
Best wishes
Roberto
On 9 Jul 2011, at 17:44, CAI Qixu wrote:
Hi,
Thank you for your suggestion.
Could you tell me what is "riding hydrogens"?
And it seems there is not "reference model" function in refmac5.6?
2011/7/9 Robbie Joosten
<[log in to unmask]>
Dear Qixu,
refamac 5.6 works well at these resolutions. You can add commands to your refinement in CCP4i by using the 'Run and view command script' (or something like that) option and just typing in the extra commands. Jelly-body has worked very well for me (although I use tigheter restraints than the default). Also local NCS works well (provided you have NCS). I never used reference structures, but I heared good things about it. Don't forget to use riding hydrogens, for some reason it is not the deafault.
Perhaps you should also switch of the automatic X-ray weighting in favour of optimizing the matrix weight yourself (start with 0.05 and compare refinements for higher and lower values).
HTH,
Robbie
----------------------------------------
> Date: Sat, 9 Jul 2011 16:59:29 +0800
> From: [log in to unmask]
> Subject: [ccp4bb] low resolution refinement
> To: [log in to unmask]
>
> Dear all,
>
> Recently, I refine two low resolution structures in refmac 5.5. Their
> resolutions are 3A and 3.5A respectively.
> For 3A structure, after MR by phaser and rigidbody refinement&restraint
> refinement by refmac5.5, I got R factor 25% and R free 35%. And then
> each time, after my model building in coot and restraint refinement by
> refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%.
> For 3.5A structure, the R factor stays 27%, but R free increases from
> 37% to 42% after my slightly model building in coot.
> Could you help me to find the reason?
>
> Maybe the reason is the overfit of the structure? I found that new
> version of refmac 5.6 has many new features for low resolution
> refinement, such as jelly boy, secondary structure restraints. But I
> don't know how to use these new features in old version ccp4i (6.1.13)?
>
> I also used phenix.refine with the "reference model" ( I have high
> resolution model for one domain of the low resolution protein) and
> "secondary structure restraints", but it seams the same. Any suggestion?
>
> BTW, is that simulator annealing not suitable for low resolution
> structure? I used the simulator annealing method of CNS and
> phenix.refine, but the geometry of the structure is always destroyed
> seriously.
>
> Could you help me?
>
> Thank you very much!
Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London
Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
