Part of what is bothering me is that the density showed up at one
exact point in the refinement, and I am currently testing what exactly
it was that changed things. To me, the blob almost looks like a mask
of the molecule, and there is very little 2Fo density, so that's
weird. I am also really bothered that the R value is so low, and yet
there's this huge blob. Something seems buggy to me. Also a
clarification: the blob runs into a two-fold axis in the middle, so
things get dodgy there too. I will let you know what I find out.
JPK
On Thu, Oct 27, 2011 at 2:53 PM, David Briggs <[log in to unmask]> wrote:
> I agree with Rafael,
>
> From those pictures it looks like a sugar chain - maybe 2-3
> saccharides in a row.
>
> HTH
>
> D
> ============================
> David C. Briggs PhD
> Father, Structural Biologist and Sceptic
> ============================
> University of Manchester E-mail:
> [log in to unmask]
> ============================
> http://manchester.academia.edu/DavidBriggs (v.sensible)
> http://xtaldave.wordpress.com/ (sensible)
> http://xtaldave.posterous.com/ (less sensible)
> Twitter: @xtaldave
> Skype: DocDCB
> ============================
>
>
>
> On 27 October 2011 17:27, Jacob Keller <[log in to unmask]> wrote:
>> Dear Crystallographers,
>>
>> In the course of a reasonably smooth refinement, all of a sudden there
>> is a huge worm-hole-type blob in the electron density (see pics). Has
>> anyone seen this before? Is it some effect of the refinement
>> over-fitting or something? For some background, resolution is 2.2Ang
>> and there are 4mol/ASU, but one of them is markedly worse in terms of
>> density than the rest, and appears to be in a non-crucial part of the
>> lattice, as if just sitting in one of the interstices. R/Rfree is
>> ~19.5/24.5.
>>
>> Jacob
>>
>> --
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: [log in to unmask]
>> *******************************************
>>
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
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