Re: [phenixbb] Maps from twinned data

I just tried the latest cci_apps and re-ran the refine job. The new version seems to clear up the problem. Thanks, Mary On Feb 1, 2008 4:05 PM, Peter Zwart wrote:

Hi Mary,

Can you try and download the latest cci_apps and recompute the maps with phenix.refine? I did make some updates since rc6 in the dewtinning code.

Cheers

Peter

2008/2/1, Mary Fitzgerald :

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Peter- I've attached an image from coot. I loaded my model and then a cns detwinned 3fo-2fc map (purple) and the 2fo-fc (blue) from phenix both are contoured at 1.5. The 3fo-2fc is the only map have at the moment equivalent to the 2fo-fc model although it had waters in the model. I have the symmetry brought up and there's not a symmetry related molecule in the area. I've been working with this model quite a while and have never seen density there before. It shows up in a couple of other spots as well with nothing appearing in the fo-fc maps, which I didn't show here. It looks as if I'm missing part of my model in areas that there shouldn't be any model.

Thanks, Mary

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Can you send a picture of the density and/or the data and model so I can have a look. The detwinning is done differently and for twin fractions of 0.5 something weird mihgt be happening.

Thanks

Peter

2008/2/1, Mary Fitzgerald :

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I'm new to phenix and just installed Phenix 1.3 beta rc6.

I've taken a data set that I've been refining in cns and am trying phenix.refine. The data has a twinning fraction of 0.5. I'm seeing what I think is odd in the 2mFobs-DFmodel.map. If I'm reading the documentation correctly, this map should be detwinned (I also set

refinement.twinning.detwin.map_types.aniso_correct=true), I

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see alot of extra density where there is no model, nor a symmetry related molecule in coot. I don't see this extra density in my detwinned 2fofc cns maps.

So, could the extra density I'm seeing be due to using a different

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and it is detwinning the data differently. The extra density is from

On Feb 1, 2008 2:59 PM, Peter Zwart wrote: program the

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twin????

Any input would be appreciated,

Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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