It's fun to watch my innocent little comment unfold into a pandemonium of
email :) That's why i love this mailing list.
Seriously though, there seems to be two salient things said by many people
in many different ways:
1. it's a good idea to look at the model in detail, and pay attention to
struc
What about the possibility of double-blind review? I have actually
wondered why the reviewers should be given the author info--does that
determine the quality of the work? Am I missing some obvious reason
why reviewers should know who the authors are?
I've always felt (and advocated long time ag
Why not double open review? If I have something reasonable to say, I should
be able to sign it. Particularly if the publicly purported point of review
is to make the manuscript better. And imagine what wonderful open hostility
we would enjoy instead of all these hidden grudges! You would never hav
Hello,
I've been struggling with F2MTZ and importing my hkl file into mtz by 'keeping
existing freeR data'. I keep getting the error "Problem with FREE column in
input file. All flags apparently identical. Check input file."
At the end of the day, it appears that this only happens in ctruncate
What about the possibility of double-blind review? I have actually
wondered why the reviewers should be given the author info--does that
determine the quality of the work? Am I missing some obvious reason
why reviewers should know who the authors are?
JPK
On Wed, Oct 27, 2010 at 5:50 PM, Phoebe R
Journal editors need to know when the reviewer they trusted is completely out
to lunch. So please don't just silently knuckle under!
It may make no difference for Nature, but my impression has been that rigorous
journals like JMB do care about review quality.
Phoebe
===
> Surely the "best" model is the one that the referees for your paper are
happy with?
That may be the sad and pragmatic wisdom, but certainly not a truth we
should accept...
> I have found referees to impose seemingly random and arbitrary standards
a) Reviewers are people belonging to a certai
Sorry I mean coordinates AND data of course.
Again, if every technically competent reviewer asks- if deemed necessary-
for coordinates and data and declines review if they are refused, that might
change.
-Nat
Ø What's to prevent your closest competitor from downloading the structure
and using it to solve and refine his or her own data?
Integrity perhaps? Ahh stupid me that is a verboten word. My original
title of the recent JApplCryst commentary was a nice alliteration -
Scientific inquiry, in
On Wed, Oct 27, 2010 at 2:20 PM, Ed Pozharski wrote:
> One can also release structure in the PDB prior to submission - I
> believe the HPUB option is rarely (if ever) justified.
>
What's to prevent your closest competitor from downloading the structure and
using it to solve and refine his or her
They do send both, if you explicitly ask as a referee and threaten otherwise
not to review, but who
a) has and takes the time to make a map and look at the parts relevant to
discussion
b) knows how to do that properly and with confidence (otherwise it’s
worthless)
A suggestion to
One can also release structure in the PDB prior to submission - I
believe the HPUB option is rarely (if ever) justified.
Ed.
On Wed, 2010-10-27 at 22:56 +0200, VAN RAAIJ , MARK JOHAN wrote:
> perhaps we should campaign for it to be obligatory to provide the pdb
> and structure factor file to the
perhaps we should campaign for it to be obligatory to provide the pdb and
structure factor file to the journal, and thus referees, upon submission? Then
he can look for himself to see that building and refinement have been performed
satisfactorily.
Mark
> Surely the "best" model is the one tha
Surely the "best" model is the one that the referees for your paper
are happy with?
I have found referees to impose seemingly random and arbitrary
standards that sometime require a lot of effort to comply with but
result in little to no impact on the biology being described. Mind you
disc
Dear Young and Impressionable readers:
I second-guess here that Robbie's intent - after re-refining many many PDB
structures, seeing dreadful things, and becoming a hardened cynic - is to
provoke more discussion in order to put in perspective - if not debunk-
almost all of these rules.
So it may
On Wed, 27 Oct 2010, Frank von Delft wrote:
So, since the experimental error is only a minor contribution to the total
error, it is arguably inappropriate to use it as a weight for each hkl.
I think your logic has run off the track. The experimental error is an
appropriate weight for the Fobs(
On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote:
> the errors in our measurements apparently have no
> bearing whatsoever on the errors in our models
This would mean there is no point trying to get better crystals, right?
Or am I also wrong to assume that the dataset with higher I/sigma
Matt-
You might want to try heating your protein to get rid of unfolded/improperly
folded protein. We have used 37C for 10 min with good success, but a time
course at different temperatures is the best way to determine which parameters
are optimum for your protein. Heat-chill it on ice-centr
Regarding the riding hydrogens:
They are obviously not visible, but your protein in solution is also not
visible but still has those weird riding hydrogens:-)
Use them, they are there. And ther was a recent compendium of neutron
scattering in one of our favorite journals if you really want to see
Anthony,
I have used the minimum of -LLfree (i.e. same as maximum free
likelihood) as a stopping rule for both weight optimisation and adding
waters, the former because it seems to be well justified by theory
(Gerard Bricogne's that is); also it's obviously very similar to Axel
Brunger's min(Rfree
Yes, but what I think Frank is trying to point out is that the difference
between Fobs and Fcalc in any given PDB entry is generally about 4-5 times
larger than sigma(Fobs). In such situations, pretty much any standard
statistical test will tell you that the model is "highly unlikely to be
correc
I've been told by my (frighteningly geek-competent) colleague that the
platters are identical, but the cheaper ones are those at the bottom of
the Quality Control pile, which are therefore spun more slowly, and
don't get any claims of reliability.
(Have you checked the disk rotation speed? I
Dear Ian,
On Tue, Oct 26, 2010 at 05:15:50PM +0100, Ian Tickle wrote:
> Yes! - the critical piece of information that we're missing is the
> proportion of *all* structures that come from SG centres. Only
> knowing that can we do any serious statistics ...
The point I was trying to make was not t
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