And given that all these maps (Fo, Fc, and their differences)
are made without the F000 term and so have average value zero,
it is highly likely that Fc will be negative in the region
of the deleted subunit (solvent is the lowest density in the model
except for the chinks of vacuum between the ato
This is hard to understand/impossible, at least in terms of
simple 2fo-fc and fo-fc maps.
We can think of a difference map as the difference between two maps,
like fo-fc map = fo map - fc map.
There is no model in the region, since you deleted it,
so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc can
A round of refinement with simulated annealing followed by minimization
should address your concern.
Pavel
On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus
wrote:
> Dear all,
> I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu.
> Molrep (template with 70 % seq identity) finds
Dear all,
I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu.
Molrep (template with 70 % seq identity) finds three NCS molecules
(the template model has only 1 chain as it is in different space
group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried
about model bias
Dear All,
thank you all for your suggestions and support. The quick look (by
removing interacting AA and subsequent refinement with and without
little SA) revealed that some AAs are mislocated and indeed seem to be
more directed to the density belonging to the ligand. So, I will try
"some" of
Dear Aleksandar,
I did use SA-OMIT map feature in Phenix, implemented by Tom Terwilliger.
I would strongly recommend you to use this feature.
Remove the suspicious residues from the pdb and run first SA-omit map in
phenix with default settings, and later with different starting
temperatures.
Make
Hi Aleks:
Maybe you can try CNS ( Initial refinement by simulated annealing) also. It may
help to get rid of the model bias and takes short time to run.
Xiaodi
> Date: Wed, 29 Apr 2015 13:52:53 +0200
> From: frederic.velli...@ibs.fr
> Subject: Re: [ccp4bb] model bias
>
Hello,
I would certainly try the "usual approaches" (map coefficients that are
less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several
of these which can be calculated). In addition, you may have a look at
the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is
If you know what residues are likely to be involved, then set their
occupancies to 0.0 (In coot go to Measures - Residue info - edit occ)
then do a few cycles of refinement with that model, and then see if there
is difference density for those residues...
Quicker than an omit map procedure.
Eleano
Dear CCP4 users,
I am currently solving a structure (2.8-2.9 A resolution) of a protein
complexed with a ligand using MR with the apo-form of this protein as
model (resolution of the model is 2.4). After MR-phasing I performed a
regular autobuild run giving me good outputs and thus I refined t
Hi Manoj,
Following on from Poul's reply, and maybe whilst you are waiting to
get derivatives ;) you could try something like the following for
getting around the model-bias-after-borderline-MR-issue.
1) generate a prime-&-switch'd map from resolve.
2) use this map to prune your model (be quite
You dont give the resolution of your data.
There are always things to check
1) space group - could it be P222 or P21 2 2 or P 21 21 2 or P2 21 2
etc etc - there are 8 possibilities.
You can use absences along the axial lines to help decide on the screw
axes, but these can be misleading if you
Great that you have MR phases - it will help you identify heavy-atom
sites for phasing and perhaps even the sulphur sites will be enough.
Poul
On 11/08/2009, at 20.33, ManojSaxena wrote:
Hi all,
I am working with a protein that have 28% similar to my MR template.
I have processed data in HKL
Hi all,
I am working with a protein that have 28% similar to my MR template.
I have processed data in HKL2000 for one of my crystal and I got unique sol in
space group
P212121. with LLG 131 and TFZ score 13.5
I have used buccaneer and coot for model building and my Rfee came to 45%.
I u
First off sorry for the cross post across bbs
I have a molecular replacement solution for a single site mutant for data
that goes out to 2.8 A.
After molecular replacement in phaser I run the following and examine the
maps for bias from the model.
Option1: simluated annealing refinement in phenix
Presumably you only want to see if the mutation has been successful, and
check for other gross changes?
It would not be sensible to try to get a well refined model from such
low resolution, espec if there is already a structure M" with better data..
So the problem of model bias in refinement is
Hi All:
There are two published x-ray structures (very similar, RMSD<1A if ignore
2 loops) available for a wild-type protein; let's call these two
structures M1 and M2. They belong to the same space group but with large
differences in unit cell dimensions (over 10%, or 10A in each dimension,
cros
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