On Wed, Jan 21, 2015 at 12:24 PM, Keller, Jacob
wrote:
>I think this will probably never happen, but maybe there could be a
> confidence value associated with each atom in structures a posteriori,
> although it might be difficult to find the right automatable criteria for
> this value. The el
On 01/21/15 15:04, Pavel Afonine wrote:
(And why not make every water into UNX for good measure as well?)
Why not indeed, except that I would not call it water but "Dummy Atom"
with an element type of your choice.
there was a time long ago when budding crystallographers were taught to
r
>
> >If you do that then what chemical type you are going to put into that
> rightmost column of ATOM record of PDB file? Note, that must be a valid
> chemical element symbol so that you can use such PDB file to calculate
> R-factors, maps and whatnot (Obviously, "X" would not work!).
>
>
>
> Why,
>If you do that then what chemical type you are going to put into that
>rightmost column of ATOM record of PDB file? Note, that must be a valid
>chemical element symbol so that you can use such PDB file to calculate
>R-factors, maps and whatnot (Obviously, "X" would not work!).
Why, Cl- of cour
>For those who insist on annotating every density blob, UNX atoms are the
> PDB's officially supported method for doing so (unless this has changed
> recently), or UNK/UNL for unknown amino acids and ligands. These are not
> without their own problems but they at least make both the presence of an
>No, I think "I don't know" is the most honest and scientifically robust answer.
It will impress at least with its solemn humility, but in this case, you *do*
know something, and that information makes the most likely answer that there is
indeed something in that blob, and that something is proba
Quote:
(I would like to do an experiment with my Cl containing data, which has Cl
sites identified by iodide data, see what would happen when resolution is
reduced and SNR is weakened)
I just realized that this experiment has an inherent problem: artificially
reducing the resolution cannot simu
Hi Jacob,
I would agree with Nat. I think with the 3A data and the local environment,
putting a Cl there is only justified by the need of supressing a peak in the
difference map. Yes the peak can really be a Cl or a water or a mixture of the
two (I would like to do an experiment with my Cl conta
On Wed, Jan 21, 2015 at 10:17 AM, Keller, Jacob
wrote:
> I see your point about not knowing that it’s a chloride, but I think you
> would agree that it is certainly more likely a chloride than map-noise, and
> perhaps more likely than water as well. Would you agree that chloride is
> the best gu
I reiterate that assigning a chloride is not “wild speculation” or “just making
something up” in light of what we know about the situation.
I see your point about not knowing that it’s a chloride, but I think you would
agree that it is certainly more likely a chloride than map-noise, and perhaps
The discrepancy between using the original mtz and an updated mtz is likely the
result of the Fobs being placed on the Fcalc scale from Refmac output, not
direct reading of Fcalc.
-YW
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller,
Jacob
On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob
wrote:
> Not sure why there is this level of suspicion about the poor halide when
> waters generally get assigned so haphazardly. I would say that there are
> probably more “wrong” waters in the PDB than wrong chlorides, but there’s
> not much fuss
I disagree with Nat—it is more likely that the blob is a chloride than a water,
and dramatically more likely than a “nothing.” And it’s certainly not “wildly
speculative,” considering that there is 200 mM Cl- in the crystallization
cocktail, and the type of contacts it makes. Not sure why there
On Wed, Jan 21, 2015 at 12:16 AM, Engin Özkan wrote:
> Carbon in chloride's coordination sphere? To me, it looks like you have
> serious vdW violations, and neither water nor chloride could go there.
>
Halides can interact with carbon too - discussed in Dauter & Dauter (2001)
- although I think
Check other Cl- in the pdb to see whether the bond lengths and VdW are an issue
(wouldn't H2O have the same VdW issues?). I am thinking (this happened to me
once by mistake) that maybe you are using the last updated mtz (output of
refinement) to refine against rather than the original one. This
Dear Ethan, Zhijie and Keller,
Thank you so much for your detailed reply! Now I think I have a much deeper
view of this problem and understand the relationship between X-ray, XFEL
and EM much better. I did learned a lot from your replies!
Best,
Chen
On Wed, Jan 21, 2015 at 7:51 AM, Keller, Jacob
Hi Rohit,
What about your Rfree? what about your protein geometry?
I will try to figure out this residual density at the realy latest step
of the refinement.
Because of your resolution, no anomalous signal available and Van der
Waals problems
it could be difficult for a referee believe in a
Phases can be deduced mathematically from a continuous transform, a la David
Sayre’s and others’ work. Compared to a crystallographic pattern, a continuous
pattern has huge amounts of information—every pixel (roxel?) would be
equivalent to a reflection, so instead of having ~10^4-5 data points y
See attached and please contact Steven Hudson (steven.hud...@nist.gov) for
more information.
=-=
Federal Post‐Doctoral Fellowship Opening: Joint project between MedImmune &
NIST
There is an immediate opening for a post‐doctoral researcher at the
National Institute of Standards and Technology (NI
But turn on the Ramachandran restraints in the box..
And ALWAYS make sure there is no obvious error before trying it - CISPEP? -
missing density etc..
Eleanor
On 21 January 2015 at 06:23, Dialing Pretty <
03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear All,
>
> Real space refinem
Hi Chen,
Here is what I think:
Assuming a crystal is perfect and is being shot at 0 K, then the maximum
resolution one experiment can achieve is limited by the wavelength of the
X-ray. It can’t be better than the half-wavelength under the normal
experimental setting (minimum d=lambda/2/sin(90)
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