[buster-discuss] Restraints

[F.Xavier Gomis-Rüth]

Thanks for the reply, Ashley, Claus, Gerard and Clemens.

The nominal resolution is 3.35Å but its is a large structure consisting 
of a dimer of >1,100 residues arranged as seven domains in tandem.

This makes the overall structure quite flexible and poorly defined for 
some domains.

We got initial phases to 4Å from a selenomethione-SAD experiment, which 
we could extend to 3.35Å.

The model is essentially ready and we are struggling with the final 
steps of refinement. Unfortunately, we do not have any reference model, 
it's a

new structure, and after each manual rebuilding step and fixing of small 
geometric inconsistencies, subsequent refinement creates another region

that needs to be fixed, and so on.

Buster performs very nicely, as usual, it is our program of choice for 
final refinement steps and map calculation. It is just that, for these 
particular

cases of low resolution, poorly defined stretches, missing density for 
side chains, etc., it would be very interesting to have an option to 
restrain

rotamers and main-chain angles to acceptable values to get the best 
model possible given these limitations. I guess this should be even more 
actual

for cryo-EM, are there any plans to adapt BUSTER to such maps?

Having said all this, we will try with the parameters you mention and 
with STARANISO.

Thanks a lot and best regards,

Xavier


On 7/2/18 15:32, Ashley Pike wrote:
>
> Xavier,
>
> No – buster doesn’t have any explicit rotamer/rama restraints as far 
> as I know. In my experience refining in the 3.4-4A range, the best way 
> to achieve such restraints is to use target restraints to a reference 
> model(s). If this doesn’t exist then it will be challenging. What is 
> the resolution you are working at? Also what is the level of 
> anisotropy – if it is anything like most of our  ‘low resolution’ 
> data, the headline number often hides even lower resolution in certain 
> directions!   Having said this, if you have a goodish input model then 
> buster normally does a really good job of keeping everything together 
> nicely.
>
> There are a lot of individual geometry parameters you could try 
> tinkering with:
>
> https://www.globalphasing.com/buster/manual/autobuster/manual/appendix1.html#SetvarParameter_GeometryWeight_names
>
> Globally you can define a rmsd bond target using –r option
>
> Cheers,
>
> Ashley
>
> *From:*buster-discuss 
> [mailto:buster-discuss-bounces at globalphasing.com] *On Behalf Of 
> *F.Xavier Gomis-Rüth
> *Sent:* 07 February 2018 11:36
> *To:* buster-discuss at globalphasing.com
> *Subject:* [buster-discuss] Restraints
>
> Dear Buster List,
>
> we are currently working with a very large low-resolution structure 
> and using BUSTER/TNT for refinement and map calculation.
>
> Given the limitation of the resolution, we would be very interested in 
> applying enhanced rotamer, geometric (for bond lengths and
>
> angles) and Ramachandran restraints, as the evaluation with MOLPROBITY 
> after each refinement cycle gives a very high number of
>
> outliers despite a good overall Clashscore (6.14; 100%) and Molprobity 
> Score (2.63; 96%). Is there a way to impose such restraints?
>
> Thanks a lot in advance,
>
> Xavier
>
> -- 
>

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