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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 your
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
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
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
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
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
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
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
