I would start with coot. As bostjan suggests - 1) choose whole chain as a
fragment.
2) fit that over chain 2 and change its label to that of chain 2. (Remember
to make this a a copy of your fragment..)
3) check is there any density for the missing bit?
Then repeat till you have the whole thing.
An
HI Pavel and all,
I’m not sure if this is what you were thinking of, but we published in 2016 a
rather dramatic example showing how a series of reliably determined extreme
phi,psi outliers document how the strain-energy associated with adopting the
phi,psi angles is distributed between an extre
>
> This is best illustrated by Ramachandran "outliers",
> which are perfectly supported by electron density.
>
Indeed, and 3NOQ is one of my favorite examples of that, an outlier isn't
necessarily equates to wrong! However, I think torsion angles (eg, phi/psi)
are much more flexible than covalent
Superimposing that molecule on all the others?
Bostjan
--
Bostjan Kobe FAA
Australian Laureate Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences
and Institute for Molecular Bioscience (Division of Chemistry and Structural
Biology) and Australian Infectious Dise
The data resolution is 2A.
I have 16 chains in my model out of which only one of the chains has the
"missing" domain modeled. Is there a way to do MR to predict where the
missing domains will go in the rest of the chains, based on my
solved structure?
Thanks for all the helpful suggestions!!
M
Well you could just try the buccaneer pipeline. It would use the phases
from your solved domain and try to fit the missing sequence. What are your
twin fractions? And what is the resolution?
Eleanor
On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote:
> Dear Medhanjali DasGupta,
> unless the resolutio
Dear Medhanjali DasGupta,
unless the resolution is really poor, the quickest try would be shelxe,
starting from what you already have. It might work at, say, 2.8A
resolution or better...
Best,
Tim
On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali
DasGupta wrote:
> Hello!
> My protein structure has a
Hello!
My protein structure has a missing domain and I am trying to figure out the
best way to model this missing domain using the solved (modeled) fixed core
domain? My data is also imperfectly twinned, with 4 twin fractions
according to refmac5.
Any help/ idea is appreciated!
--
Thanks,
Med
On 09/11/2022 13:59, Deepak Deepak wrote:
Dear CCP4 users,
I am working towards solving a protein-ligand complex structure. The
ligand is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive
monomers. [...]
I will happily provide more information if I am missing something here.
You're
Dear CCP4 users,
I am working towards solving a protein-ligand complex structure. The ligand
is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive monomers. I
have a PDB model for the ligand and also as smiles and mol2 format.
I tried generating restraint files for this ligand using Jligand,
This year the CCP4 Study Weekend will be held as a hybrid event from the 4th -
6th January at the East Midlands Conference Centre, Nottingham, UK, with an
exciting programme confirmed below. Early bird registration is open until 13th
November, more details of which can be found here:
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Dear all,
what I am missing in this whole thread is the question
on what is the "true" value of a given bond distance. So
far, everybody seems to assume that the "ideal" value
is equivalent to the "true" value, and that deviations
from the ideal values must therefore be outliers.
I challenge th
And now it is time for an "old man story". Back in the early 1990's
the Brookhaven PDB started to worry about "validating" the models being
deposited. One of the things they implemented was to add to the header
of the PDB a complete list of all bond lengths and angles that deviated
from th
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