> Point #2 would hold if we routinely let our refinements run to
> convergence; seems common though to run "10 cycles" or "50 cycles" instead
> and draw conclusions from the behaviour of the metrics. Are the conclusions
> really much different from the comparison-at-convergence you advocate?
> Wh
Hi Ian
(Yes, your technical point about semantics is correct, I meant
over-fitting.)
To pin down your points, though, you're saying:
1) Don't use Rfree, instead look at LLfree or Hamilton Rfree.
2) Compare only the final values at convergence when choosing
between different parametriz
Dear colleagues,
I would like to draw your attention to an upcoming free, educational webinar to
be presented by Jim Pflugrath, Ph. D. titled "An Insider's Guide to
CrystalClear and d*TREK: Improve Your Results with these New Features and
Tips". In this webinar, Jim will discuss three important
Successful complexation depends on the
concentration of protein, ligand, and the Kd of the protein-ligand
complex. For Kd>>[protein], you will probably require
[ligand] > 10 x Kd. As Kd approaches [protein], slightly
superstoichiometric quantities will be sufficient f
Dear All
I quick reminder - last chance to sign up for the 2nd MX User Workshop at
Diamond - the workshop is part of the Synchrotron User Meeting, September
7th-8th, 2011. Workshop sessions include presentations from staff and users on
latest developments, spectroscopy, crystal dehydration and
Dear Greg,
Try ARP/wARP 7.2, released a few days ago, which is better, more
stable and should have improved flash of error messages to the log
files.
ARP/wARP Loopy will not build a 33-residue loop at once, but Classic
model building may get the gap shortened.
Go to www.arp-warp.org for
Time to start digging in the archives. Try looking at work by Fran
Jurnak in 1986 (J. Cryst. Growth 76, 577) and Bill Ray's work in 1985
(Analytical Biochem 146, 307), and then the works that cite them. I
thought this was common knowledge, but I guess it goes in phases.
Aging of poly(olig
Calculate - Merge Molecules
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
jab
Sent: Thursday, August 25, 2011 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] merge chains in coot
Hi
I've tried to find where to merge chains in coot,
Hi
I've tried to find where to merge chains in coot, eg merge built co-factor
to protein chain, or
merge all my ions (Na, Cl, Mg etc) together.
Any pointers?
Thanks
Jim Brannigan
Dear TY,
Typically between 5-10x molar concentration over the protein is enough to
ensure binding when the IC50 is uM to low mM. For tighter binding compounds (nM
to low uM), 2-5x is sufficient. Whatever you do, when the precipitate occurs DO
NOT REMOVE it. I learned to my chagrin that you ch
Hi YT-
We normally prepare our ligand stocks in DMSO and add this to the protein in
3-fold molar excess. The majority of our ligands are quite insoluble and
precipitate when the DMSO concentration decreases upon addition to the
protein... so I am not surprised that you are seeing this. I
Hi all,
I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of
the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6).
I can see some broken up density at one end, but have been unable to
convincingly build into into this region manually. I would
Hi Frank
> This is self-evident; what is not obvious is why the target function
should be having the final word. Wasn't the word "over-refinement"
introduced to describe exactly this: that the target function was wrong?
I assumed people were confusing 'over-refinement' with 'over-fitting'; the
Hmm, I used to think I understood this, but I'm feeling a bit dim right
now.
On 25/08/2011 11:07, Ian Tickle wrote:
Since the target function in MX refinement is the total likelihood
(working set + restraints), there's no reason whatsoever why any
another function, such as Rfree & LLfree, shou
TIm,
I dare say that the goal is to get phases which match as good as
> possible with what is inside the crystal. If this coincides with
> maximising the likelihood, why don't we run refinement until the LL
> stabilises?
>
That's exactly what you should do: any optimisation procedure attains the
Hi all,
Thanks for the suggestions! Anyway, the problems have been fixed! When I
edited the CIF files in a mac editor, the file formatting got changed, so a
line feed became a carriage return and Coot does not like this as to it they
appear to be different files.
The CIF files were fixed by using
Hello Tim
It was in one or two versions and I did not get consistent results. However
code is there and I can activate it if you want. If you know what criteria you
would like to use I can code that also.
In some cases it happens that R/Rfree go up and then they start coming down. It
may be ca
Dear,
We're wondering what tools there are available in order to estimate
the 'melting point' and 'heat of fusion' from a known crystal
structure (e.g. coordinate file)..?
It concerns mostly small molecules (> 100 atoms).
Many thanks
Kristof
---
Kristof Van
Did you rename the ligand in the CIF file as well? It would be nice if the Prodrg interface allowed you to type in the
name of the ligand you want in the CIF and PDB file. Hopefully a global replace in your favourite text editor of DRG
with LIG or whatever you want to call your ligand would wor
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Hash: SHA1
Hello Ian,
I dare say that the goal is to get phases which match as good as
possible with what is inside the crystal. If this coincides with
maximising the likelihood, why don't we run refinement until the LL
stabilises?
@Garib: I have seen runs wher
for me, I prefer to sock these compounds into your crystal. it will much more
easy than co-crystallizaiton. But each protein should be different.
Normally when I star to co-crystallization with small compound, I will set up
the complex with 1:1.2 molar ratio as first trial to see what should hap
We offer 4 Postdoctoral Positions in Structural Biology in Geneva
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These positions are available immediately in the laboratories of Profs.
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