On Thu, 2011-10-27 at 20:46 -0500, Jacob Keller wrote:
> I went back to using
> the original mtz from scala
Curious. What were you using - the refmac output mtz? Just for the
record - the refmac output mtz contains *modified* amplitudes, and Garib
said many times it should not be used as the in
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Hello Jacob,
On 10/28/2011 03:46 AM, Jacob Keller wrote:
> Blob is gone--something funny happened, I guess. I went back to using
> the original mtz from scala, removed and replaced a bunch of waters,
^^^ maybe that solves you
Weird. It's pretty much exactly what a nonbranched sugar (triose, in this
case) would look like.
were the dimensions consistent with three sugars? were there any collisions
with backbone or side chains inside/near the mystery density?
It really looks like maltotriose... is the protein a sugar bind
Blob is gone--something funny happened, I guess. I went back to using
the original mtz from scala, removed and replaced a bunch of waters,
and no more worm! I can't really figure it out, and wish I knew
exactly what happened, but I think I am just going to non-chalantly
move along.
Jacob
On Thu,
Jacob,
By simply looking at the figures you show, it does look like you have some type
of long, maybe polymeric, molecule bound.
With that being said:
1- It is in the symmetry axis so maybe be a little noisy there
2-If you are in doubt about it being real or not check the density and how it
fits
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 both
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:
david.c.bri...@manchester.ac.uk
==
Maybe sugars?
El 10/27/11 6:27 PM, Jacob Keller escribió:
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-fittin
