Your split between Rfree and R suggests you are using refmac. (I also
got a hint when you explicitly said you were using refmac.) Although
there are many efficient ways to get stuck in a refinement, I have
found the most effective by far is underweighting the structure
factors and falling into the viscous cycle of model bias, which is why
I have religiously avoided refmac in the past. Try upping the
"weighting term" from the default of 0.3 and building into the maps
that result. I got this latter advice recently from our x-ray admin
who was also kind enough not to give me a forehead slap for my
cluelessness.
James
On Apr 15, 2009, at 2:39 AM, ANDY DODDS wrote:
> Hi James,
>
>
> I usually use DM in teh CCP4 suite to do DM. It gives you options to
> do solvent flattening, Histogram matching and NCS averaging.
>
> If you compare the FOM to the DMFOM in the mtz files, you can usually
> see and improvement in the score. That is usually all I bother my
> arse to look at. Any comments as to what else I should be looking at
> generally, would be welcomed.
>
> I am currently working on a difficult structure at 2.9 Angstrom that I
> cant get to lower the RFree any more and am stuck at 32% with a R fact
> of about 21%. I went back and performed density modification right at
> the start, then performed MR and the same refinement as before and saw
> absolutely no improvement in refinement statistics at all. They were
> identical using the non-DM modified mtz file. I was surprised, but
> this may be due more to the fact that I don't fully appreciate what is
> going on here.
>
> For the record I performed flattening and matching and tried this and
> then both plus NCS (there is NCS in my model) averaging and still
> absolutely identical refinement statistics. This is using refmac by
> the way TLS + restrained refinement.
>
>
> Sorry for the thread hijack James, but at least it is related! ;)
>
> cheers
>
> andy
>
> 2009/4/15 James Stroud <[log in to unmask]>:
>> Hello All,
>>
>> What is the current state of the art with respect to density
>> modification
>> after molecular replacement? In other words, what programs are
>> people having
>> the best luck with these days?
>>
>> Thanks in advance for any hints.
>>
>> James
>>
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