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Re: [ccp4bb]: averaging structures



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rams@poori.biochem.uiowa.edu wrote:
> 
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> 
> Hello All,
> 
> I remember this question being asked in a different context - but I did
> not find the answer so here I go again!
> 
> I managed to solve a structure using an NMR ensamble and Beast.  I also
> manage to do the same with AMoRe (the Navaza version - the ccp4 version
> does not seem to do it).  I cannot seem to get the structure with one
> model - so thats fine.  I think the solution is correct as it is
> significantly higher in cc than the others.  Packs well.  The space group
> could be p4x2x2 and I get clear values for x - i.e., I can solve the
> structure only in p43212. So, I am happy :-)


 Re CCP4 Amore - I thin kit stops reading coordinates at the end of the
first model - at least in one set of coordinates we had there wasan END
stt, and the program obeyed it - ie ENDed reading! 

> 
> Trouble starts when I begin to refine.  I have tried refining with refmac
> and one model.  CNS with one model.  dm after rigid body refinement etc..
> and several starting models.  In every case, I end up producing maps that
> are good and bad (I can always see some side chains that show up clearly
> after throwing in a poly Ser model).  So, that gives me confidence.
> 
> My data is good only to 2.2A resolution (crappy data to 1.8 available).  I
> have tried warp and resolve too.. Nothing seems to do well.  So, what I
> want to do is simply calculate phases from each one of the NMR models
> and average then "warp style" and calculate maps.  Is there a nice way to
> do it ?
> 


 This is theoretically the same as calculating SFs with all models
overlapped, then generating the map..

 You could use SFALL or better REFMAC5 which will give the SigmaA
weighting, to do that ( Refmac NCYC 0 ..) 

>   Eleanor

PS - when you work out a protocol let the rest of us know!