All,
We have been following the CCP4BB discussion with interest. As has been
mentioned on several occasions,
the JCSG has maintained, for several years now, an open archive of all
diffraction datasets associated with
our deposited structures. Overall this has been a highly positive experienc
-Original Message-
From: James Holton
To: CCP4BB
Sent: Tue, Nov 1, 2011 11:07 am
Subject: Re: [ccp4bb] Archiving Images for PDB Depositions
On general scientific principles the reasons for archiving "raw data"
all boil down to one thing: there was a systematic error, and yo
Clemens,
In the past, we have used TRACER (free domain) for higher symmetry or we
interpreted manually Niggly values :-)
TRACER is gone long time ago. Niggly values are not displayed anymore, so we
trust auto indexing of DENZO which, assuming all experimental parameters are
properly set ( we
God bess the symmetry, we are saved from the over-interpreting symmetry
(except probably of very exotic cases) by the very high Rsym factors around 40%
50% if the symmetry is wrong.
Even wild rejection of outliers, cannot reform "acceptable" Rmerge.
In my personal repository, 1QZV is a manifest
On Thu, Nov 03, 2011 at 04:13:44PM -0400, Bryan Lepore wrote:
> not sure I follow this thread, but this table might be interesting :
>
> http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf
>
> from:
>
> Detection and correction of underassigned rotational symmetry prior to
> struc
not sure I follow this thread, but this table might be interesting :
http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf
from:
Detection and correction of underassigned rotational symmetry prior to
structure deposition
B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Saut
Hi James,
scary ... I was just looking at exactly the same thing (P21 with
beta~90), using the same tool (POINTLESS).
Currently I'm going through the structures for which images can be
found ... I haven't gone far through that list yet (in fact actually
only the first one), but this first case sh
I tried looking for such "evil symmetry problem" examples some time ago,
only to find that primitive monoclinic with a 90-degree beta angle is
much more rare than one might think by looking at the PDB. About 1/3 of
them are in the wrong space group.
Indeed, there are at least 366 PDB entries
On 11/01/11 16:32, Anastassis Perrakis wrote:
An experiment that I would like to do as a structural biologist - is the
following:
What about adding an "increasing noise" model to the Fobs's of a few datasets
and re-refining?
How much would that noise change the final model quality metrics and
Hi Ed,
Ok, I'll bite: I would be very interested to see any data sets which
initially were thought to be e.g. PG222 and scale OK ish with that but
turn out in hindsight to be say PG2. Trying to automatically spot this
or at least warn inside xia2 would be really handy. Any
pseudosymmetric examples
On general scientific principles the reasons for archiving "raw data"
all boil down to one thing: there was a systematic error, and you hope
to one day account for it. After all, a "systematic error" is just
something you haven't modeled yet. Is it worth modelling? That depends...
There are
Dear Gerard
Isolating your main points:
but there would have been no PDB-REDO because the
data for running it would simply not have been available! ;-) . Or
do you
think the parallel does not apply?
...
have thought, some value. From the perspective of your message,
then, why
are the bene
Gerard Bricogne wrote:
. . . . the view, expressed by many and just now
supported by George, that developers could perfectly well do their job on
the basis of relatively small collections of test datasets that they could
assemble through their own connections or initiative. I mostly agree with
t
Dear Tassos,
If you apologise for a long e-mail in a long chain of them, I don't
know with what oratory precautions I should preface mine ... . I will
instead skip the disclaimers and try to remain brief.
It seems to me that there is a slight paradox, or inconsistency, in
your position.
Speaking as a part-time methods developer, I agree with Tassos that a couple
of hundred suitably chosen and documented datasets would be adequate for most
purposes. I find that it is always revealing to be able to compare a new
algorithm with existing attempts to solve the same problem, and this
To avoid misunderstandings, since I received a couple of emails already:
Is it important to make such a resource available to developers?
Absolutely?
? was a typo. I meant Absolutely!
I think such data are essential for development of better processing
software, and I find the development
Dear all,
Apologies for a lengthy email in a lengthy chain of emails.
I think Jacob did here a good job refocusing the question. I will try
to answer it in a rather simplistic manner,
but from the view point of somebody who might only have relatively
little time in the field, but has enjoyed
Dear Adrian,
On Mon, Oct 31, 2011 at 06:29:50PM +0200, Adrian Goldman wrote:
> I have no problem with this idea as an opt-in. However I loathe being forced
> to do things - for my own good or anyone else's. But unless I read the tenor
> of this discussion completely wrongly, opt-in is precisely
"Loathe being forced to do things"? You mean, like being forced to use
programs developed by others at no cost to yourself?
I'm in a bit of a time-warp here - how exactly do users think our
current suite of software got to be as astonishingly good as it is? 10
years ago people (non-developer
Pilot phase, opt-in--eventually, mandatory? Like structure factors?
Jacob
On Mon, Oct 31, 2011 at 11:29 AM, Adrian Goldman
wrote:
> I have no problem with this idea as an opt-in. However I loathe being forced
> to do things - for my own good or anyone else's. But unless I read the tenor
> of
I have no problem with this idea as an opt-in. However I loathe being forced to
do things - for my own good or anyone else's. But unless I read the tenor of
this discussion completely wrongly, opt-in is precisely what is not being
proposed.
Adrian Goldman
Sent from my iPhone
On 31 Oct 2011
Dear Crystallographers,
I am sending this to try to start a thread which addresses only the
specific issue of whether to archive, at least as a start, images
corresponding to PDB-deposited structures. I believe there could be a
real consensus about the low cost and usefulness of this degree of
arc
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