Matthew:
I think your nice summary leaves out an important point that has not been
explicitly mentioned. That is the question of whether depositing hydrogens
actually adds information to the model. I submit that for a typical protein
refinement it does not. The model is adequately described by s
Dear Diana and CCP4BB subscribers,
I apologize for the mess created by our recent communication with Diana. The
misunderstanding occurred because my replies to “ALL” went to senders, but were
not posted at the CCP4BB site. This happened because my email address changed
recently. As a result, Di
My structure contains riding hydrogens because (surprise!) the protein contains
hydrogens, no matter the resolution of the data. Hydrogens should contribute to
the calculated structure factors, because they do contribute to the observed
structure factors. If I delete the hydrogens from the coord
On Friday, 28 February 2020 11:19:37 PST Diana Tomchick wrote:
> If you deposit an mmCIF file that contains both the observed and calculated
> structure factors from your final round of refinement, then the PDB
> auto-validation reports the same (or so close to the same as to be
> negligible) R fac
Dear All
there is one week left to apply to this exciting PhD opportunity to work with
my colleague Chris Prior on:
Developing reliable ab-inito software for the interpretation of protein
structure from BioSaxs data
https://www.findaphd.com/phds/project/developing-reliable-ab-inito-software-for
We should demand that the wwpdb discards all entries that do not satisfy the
“the criteria of I/SigI > 5 and Rmerge <50%” good practical reference” 😊 .
That’s probably a majority of them. And of course all associated pubs should be
retracted, to be consistent with the referee’s attitude of refus
If you deposit an mmCIF file that contains both the observed and calculated
structure factors from your final round of refinement, then the PDB
auto-validation reports the same (or so close to the same as to be negligible)
R factors.
Phenix outputs all of this automatically for you if you click
On Thursday, 27 February 2020 16:34:50 PST Alexander Aleshin wrote:
> Ethan wrote:
> - If you are not making claims about hydrogens but just want to
> describe what you did during refinement, I'd go with taking them out
>
> I've noticed that REFMAC and Phenix use riding hydrogens to calculate
Which molecular dynamics package are you using?
-James Holton
MAD Scientist
On 2/28/2020 7:00 AM, Firdous Tarique wrote:
Hello everyone
I am trying to run a molecular dynamics simulation of a protein which
has a Zn atom and few phosphorylated PTMs (Thr is phosphorylated).
PTMs and Zn play es
Dear Colleagues
I would like to recruit a post-doctoral fellow with an interest in protein
structure to my group at the Salk Institute. We are developing Sonogenetics
using ultrasound to non-invasively control target cells within the body. We
have identified a number of such proteins and would l
I fully agree with this!
Best, Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Phoebe A. Rice
Gesendet: Freitag, 28. Februar 2020 17:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] What resolution - X-ray diffraction round this
time
EXTERNAL : Rea
But that wouldn’t incorporate other useful information, such as percentage
completeness in the outer shell and whether inclusion of the reflections in the
outer shell for refinement actually effects the resulting structural model and
map to a significant degree.
Diana
*
Can we get some momentum for the "standard table 1" including TWO numbers -
outer limit used in refinement, and nominal resolution based on some standard
such as I/sigI =2 (or 3, or whatever the community can agree on)? That would
hopefully cut down on all the reviewer complaints of overstated
Dear all,
We are recruiting for a new member of the CCP-EM team:
https://www.harwellhub.com/Jobs/2020/February/Computation-Scientist-CCP-EM-Software-Developer-fo
This is a really exciting software development post working in collaboration
with Sjors Scheres (MRC-LMB, RELION) and Gerard Bricogne
Dear colleagues,
I agree with all the previous responses, it is a pity to throw away
useful high-resolution data. The problem of high-resolution cutoff
estimation is also nicely summarized in another paper by Andrew Karplus
and Kay Diederichs "Assessing and maximizing data quality in
macromolecula
Dear all,
Please note the approaching deadline for Call for Regular Proposals for PETRA
III beamline P11.
This call relates to beamtime during July-December 2020.
The deadline for PETRA III proposal submission is
--
2 March
Ask the referee - (apart from the other suggestions here)
‘How would removing data Improve my model?”
Sent from my iPad
> On 28 Feb 2020, at 08:22, dusan turk wrote:
>
> Hi,
>
> Browsing through the recent discussion on EM data resolution cutoff it
> occurred to me that the X-ray diffractio
Hi, Firdous,
Most modern force fields have a way to describe ions, small molecules or
modified residues for MD run. And they already contain description for
phosphorilated aminoacids. So you can choose whichever you want.
But it is more appropriate to ask in the specialized mailing list, like
CCPBi
Tell the editor to find a new reviewer. And cite Kay's paper, the one
Graeme linked to.
On 28/02/2020 08:22, dusan turk wrote:
> Hi,
>
> Browsing through the recent discussion on EM data resolution cutoff it
> occurred to me that the X-ray diffraction community isn’t that unanimous
> either.
>
Hi Dusan,
I don't know what the correct answer is but I think it is safe to see that your
referee has outdated views (trying to stay polite here). I/sigI > 2.0 with
decent completeness would be not be seen as to agressive by most (but as too
conservative by others!). From that cut-off you could
Hi Dusan,
I am pretty sure
"It is well accepted that the criteria for resolution cutoff should consider
both I/SigI and Rmerge for the outer most shell. For data sets collected at
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as
a good practical reference.”
has
Hi,
Browsing through the recent discussion on EM data resolution cutoff it occurred
to me that the X-ray diffraction community isn’t that unanimous either.
My stand:
When the default resolution cutoff provided with the data processing software
in electron density map calculation and refinemen
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