Dear Eric,
For your question 2, the following paper provides some examples:
Acta Cryst. D63, 793-799 (2007).
In one of the examples, there is shown a partial model from Phaser
containing ~20% residues in the ASU can be extended to more than 90% of the
ASU by the iteration of ARP/wARP-OASIS-DM. D
Dear friends of the Fourier transform,
I am refining a structure with 2 adjacent Hg atoms bound to cysteines of
different monomers in the crystal contacts, which means I need to refine
them as well. While the structure nicely refines (2.2 A data), I do not
get rid of negative density ripple la
There are many many kinases with different conformations of the C
terminal and N terminal domains.
I would first refine the Cterminal as far as you can go - correct the
sequence etc etc.
Then align a selection of kinases on your C-terminal coordinates (
MSDfold at www.ebi.ac.uk/msd will return
Well - there will be a ripple, but is it there in the difference map as
well? that is meantto be less affected.
REFMAC5 claims to be able to refine some atoms anisotropically and
that would be a good place to start
Maybe you will need to read the documentation! There is some way of
request
On Wed, 2007-08-01 at 09:35 +0200, Klemens Wild wrote:
> Dear friends of the Fourier transform,
>
> I am refining a structure with 2 adjacent Hg atoms bound to cysteines of
> different monomers in the crystal contacts, which means I need to refine
> them as well. While the structure nicely refin
Klemens Wild schrieb:
Dear friends of the Fourier transform,
I am refining a structure with 2 adjacent Hg atoms bound to cysteines of
different monomers in the crystal contacts, which means I need to refine
them as well. While the structure nicely refines (2.2 A data), I do not
get rid of neg
You've most likely looked at this, but if not it might be worthwhile to
check how these ripples behave while varing the low-resolution limit used
(20-2.2,15-2.2, etc).
Pete
> Dear friends of the Fourier transform,
>
> I am refining a structure with 2 adjacent Hg atoms bound to cysteines of
> diff
Hi Klemens,
As friends of the Fourier transform we hate to see it truncated.
Although others don't think this is your problem I personally think it
very well may be. To get a truncation effect you must first have
truncated your data.
- Is the I/SigI of your highest resolution data in the 1-2
> If your Phaser results show a high Z-score (> 8) AND high LLG AND your
> solution packs without clashes AND refines (even though starting R/Rfree
> is high) AND reproduces density for the model portion AND produces some
> Fo-Fc density for the missing portion, most probably your solution is
> cor
Although I would certainly try refining just Hg anisotropically and think
that truncation ripples are very likely, you should also take into account
that mercury derivatives are particularly sensitive to radiation damage.
Often the Hg atoms have departed (but may still be in the vicinity) before
Bart Hazes schrieb:
...
W.r.t. Kay's reply I think the argument does not hold since it depends
on how badly the data is truncated. E.g. truncated near the limit of
diffraction will give few ripples whereas a data set truncated at I/SigI
of 5 will have much more servious effects.
Bart
Bart,
Sorry Kay,
I completely agree with you and should have read your message more
carefully before jumping to conclusions. I thought you suggested the
ripples where not strong enough ... I'd better have my coffee now :)
Anyway, I don't think I wasted your time because your expanded
explanation o
I have seen similar ripples with S-methylmercury cysteine - and an 80
sigma peak for Hg is not that surprising! Anisotropic refinement was
not helpful in reducing the ripples, as it is indeed a summation
problem. It's a good idea to refine occupancy of the Hg, though, and to
look for dual con
If you are refining against data from near the Hg edge (1.01 A), then
you are most likely using an inappropriate scattering factor for Hg. At
the edge, as much as 25% of the electrons are "missing" (scattering out
of phase). As GMS pointed out, there could also be radiation damage,
which mean
Eric Pettersen wrote:
> On Jul 21, 2007, at 11:12 AM, Joe Krahn wrote:
>
>> Another problem is that the original meaning of HET groups continues to
>> be corrupted. ATOM records are for commonly occurring residues from a
>> list of standard residues.
>
> No, they're for commonly occurring _polyme
Hi All,
Here are the summary from all the answers to my questions:
1. Try use arp/warp to build the missing part of structure.
2. Build as much as possible for the missing part and the current c-terminal
domain, using as low as 0.5 contour of the 2Fo-Fc density. Generate mask and
then do averagin
So, I am thinking about putting up a survey somewhere to get a measure
of the user-communities interests, because RCSB and wwPDB seem
uninterested in doing so. Maybe a group result would be more useful in
influencing the standards. I am hoping that the wwPDB can become a
better place for format sta
On 1 Aug 2007, at 22:55, Eric Liu wrote:
Hi All,
Here are the summary from all the answers to my questions:
1. Try use arp/warp to build the missing part of structure.
I have to clarify to avoid misunderstandings, that :
1. ARP/wARP autotracing is a bad way for building difficult parts
2.
Dear colleagues,
I would like to thank J. Murray, J. Wright, K. Futterer, E. Dodson, A. Forster,
and F. Long for responding to my posting of two days ago on pseudo-translation
vectors in molrep vs other programs (see original posting at the end of this
message).
I should have said at the outset tha
I was present at the creation of what is called the "PDB"
format in the mid-1970's and HOH was always HETATM. The only
thing special about HOH was that we felt that it was not
necessary to include a HET record in (virtually) every entry
to define HOH.
We felt that it would be useful to
On Wednesday 01 August 2007 14:10, Joe Krahn wrote:
> In addition to questions about the PDB standard, it is probably
> important to consider mmCIF. One thing I don't like about it is that
> columns can be randomized (i.e. X, Y, and Z can be in any column), but
> the mmCIF standards people have no
I suspect this will be throwing fuel on the fire, but what is so great about
the PDB format (any version) besides familiarity? It seems to me to be
outdated, inadequate and generally mis-used by all. I say scrap it, make a
clean break and devote everyone's energies to making a format that wil
> ...One thing I don't like about it is that
columns can be randomized (i.e. X, Y, and Z can be in any column)
Rows too! Some anarchists even re-order the symmetry operations ;-)
-Jon
Ethan Merritt wrote:
> Examples include:
> - very large structures, for which the current 80 column PDB format
> runs out of space for atom numbers (4 columns -> max )
> or for chain ids (1 column -> single char A-Z 0-9)
> [don't ask my why they don't want lower case]
> - new classes of ex
Perhaps in one of the early reported attempts to refine an Hg derivative
we did the anisotropic refinement and we reported something of the
anisotropy (Hg derivative at a Cu site) in the methods. The quality of
the data "allowed" for this (1.9 A resolution, for instance) even though
we ended up de
Hi Joe,
as both a contributor to the data and a user of the PDB files, I think you
are a bit harsh in the general extrapolation of your frustration with PDB.
I have communicated with the PDB folks both at Rutgers
and at EBI extensively about many of the shortcomings in both deposition
and data m
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