In this sort of case, I find that often the Rama-bad residues appear unfixable
because small distortions in many bond lengths and angles have made the side
chain appear correctly fit even though the rotamer choice was wrong.
My recipe for fixing that:
* Mutate the offending residue to glyci
Dear Ezequiel,
Be careful, it also happens that the asymmetric contains two half-dimers, with
the other half of the dimers being generated by crystallographic operators.
In this case it is not possible to rearrange the monomers such that the
asymmetric unit contains one biological dimer and for
Dear Tereza,
First, a shameless plug for ISOLDE (https://isolde.cimr.cam.ac.uk). It’s built
specifically for working with models around your resolution.
Other than that, I’d suggest having a close look at the corresponding sites in
your high-resolution reference models as a sanity check. Rememb
Dear Tereza,
In certain cases it could be better to do a step back to be able to
rebuild properly.
Did you look carefully in the real-space the agreement between your
model and the visible density.
If you "over"refined your model in reciprocal space only you can loose
some information.
I
Hi
Just to make sure about this - you do NOT need to reprocess the data (i.e. You
don't need to repeat the indexing) you only need to change the space group in
the way that Eleanor has indicated.
Harry
--
Dr Harry Powell
> On 7 Mar 2019, at 21:36, Eleanor Dodson
> <176a9d5ebad7-dmarc-req
Thank you for your comments.
1) manual correction in Coot does not work - the density is too weak
2) manual NCS is substantially better than automatic local NCS in this case
3) CPP4i2 might be good idea
4) PDB REDO is great, however no more help in this case
5) Prosmart - I use "prosmart -id -p1 t
Dear Tereza,
It is highly recommended that you do not attempt to directly optimise the
Ramachandran plot during refinement. Doing so would not guarantee you a better
model, and would mean that you could no longer use the Ramachandran plot for
validation purposes.
I suggest that you inspect eac
Hi Tereza,
Rather than opting for a technological fix in a reciprocal space refinement
program you should look at all the outliers in Coot and see if they are
fixable. If they are severe outliers, you need to rebuild by peptide flipping
and possibly by more invasive actions. If you have small o
Dear all,
I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB
structures (identical molecules with high resolution) and I use NCS, medium
between AB (prot
Dear Murpholino
Unfortunately no rule of thumb has been established, although I have only seen
contraction once and have seen expansion for very many proteins.
Seems to depend critically on the particular crystal (and probably its density
of stacking imperfections/dislocations) and even crystals
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