Well, perhaps my inquiry to Anatrace for such a resource (wiki?) will work
out. It was suggested to me that I thus inquire by somebody on this list.
They probably have a lot of data which they have not published anywhere, for
whatever reason. Hope that won't scoop you, or perhaps you would be wi
I have found Bob Laughlin's book 'The Aqueous Phase Behavior of Surfactants' to
be a useful resource on detergents. It has several relevant phase diagrams.
Heavy on the P. Chem.
Then there is the mother of all info in the area "Critical micelle
concentrations of aqueous surfactant systems" a
There is a series of books - Surfactant science series which has some
of this information. I'm familiar with the Nonionic Surfactants,
Anionic Surfactants, and Cationic Surfactants books (they have
unattractive green covers) from the days when I used to work for a
soap company.
One probl
Hi Dirk,
Nice cross validation flags for twin refinement do obey the twin law:
if (h,k,l) is in the free set, then (k, h, -l) should be as well.
Same is/should be true for work set btw.
In phenix, we generate test reflections that follow the lattice
symmetry (*). This means that even if you do n
Hi,
The only published compendium on detergents still available (to my
knowledge) is http://www.merckbiosciences.co.uk/docs/docs/LIT/CB0068_M.pdf.
No phase diagrams though.
Regards,
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
UHP - Nancy 1, School of Medicine
try using phenix.refine and use TLS. it might help lowering Rfree (or
raising Rwork).
P
2007/10/23, john kryst <[EMAIL PROTECTED]>:
> Hi CCP4bb ,
>
> Thanks for your suggestions... here is the summary of the
> structure...
>
> I am working in deletion and point mutants. I have a
Hi John,
if I understand the "make_cv_twin.inp" correctly, then this script
takes care about separating reflections related by the twin law to
avoid a potential bias of the Free-R set with twin-law-related
reflections from the working set. At least, in the source of this
script I read the
1) How can I make a mask as mentioned above? Am I doing it the
wrong way?
You can run NCSMASK with your first placed domain and generate a
suitable mask file for DM.
2) Is there any other method to improve the density of the
missing structure? I tried several MR probes of the sec
Hi
Have you checked for twinning?
J
TC Hu <[EMAIL PROTECTED]> wrote:>
> Dear all,
>
>
>
> I am working on a structure which is composed of two domains. The X-ray
> data
> is quite good (P21, 2.2A, Rmerge=0.08, 93% completeness), there is one
> molecule (277 residues) per ASU. The structure h
Yes, I should explain better "that might not justify all your
observations"; in more details, if such care (free set considered the twin
law) was not taken it is probable that the gap between R and R-free is even
larger, as Anastassis points. Might R-free become a "reasonable" value in
this
But, if that was the case, wouldn't you expect the opposite, Rfree to
be too close to R ?
here they appear to be too different !
in other words: if Rfree is not 'really free due to twin law' i would
expect R/Rfree to be too close, not too far !
A.
On Oct 23, 2007, at 13:58, Jorge Iulek wro
Hi CCP4bb ,
Thanks for your suggestions... here is the summary of the
structure...
I am working in deletion and point mutants. I have a mutant (P61 resoln
3.1A) with partial twinning with twinning fraction 0.28. Wilson b-factor is
50. The data collected in the home source with norma
Apologies (once again) for the non-CCP4 nature of the advertisement
below - Gordon
The Partnership for Structural Biology (PSB) is an international
consortium comprising the European Synchrotron Radiation Facili
The R and Rfree after refining domain 1 are 39% and 44%. The
density is good for the existing model but disconnected in the
missing part of the structure in which I can hardly place any residue.
2) Is there any other method to improve the density of the
missing structure? I tried sever
Jacob,
Actually, there is no real definitive compendium of detergents and
their properties (solubility, CMC, aggregation number, etc.).
Because of their importance to industry, commercial compendia, as
Anatrace's catalog, are often the most complete. However, most
commercial compendia a
Dear all,
I am working on a structure which is composed of two domains. The X-ray data
is quite good (P21, 2.2A, Rmerge=0.08, 93% completeness), there is one
molecule (277 residues) per ASU. The structure has four homologous
structures with sequence identities ranging from 35%-40%. The four
stru
Hi,
How good/bad is the geometry of your model (as judged by the usual criteria
either in procheck of molprobity) ?
Boaz
- Original Message -
From: john kryst <[EMAIL PROTECTED]>
Date: Tuesday, October 23, 2007 7:04
Subject: [ccp4bb] Twinning
To: CCP4BB@JISCMAIL.AC.UK
> Hi cc
John,
One other point to be added, although that might not justify all your
observations, is to be sure that the R-free set was chosen respecting the
twin law. Both phenix and CNS (not automatically) can do this. Of course, as
pointed before, when you change your R-free set, you should "ann
Hi Sabine,
in addition to what Christian has written, please, also check whether
the ribose atom names contain a "*" instead of "'" to conform with
the PDB convention.
Best regards,
Dirk.
Am 22.10.2007 um 21:37 schrieb Christian Biertumpfel:
Hi Sabine,
Your problem might be an issue of
There might be a few reasons for these R-values which seem to contradict
experience:
1) The starting phases result from MR where the model is very close and
from a data set at higher resolution. If your 3.1A data are of
respectable quality, the model would still correspond well to the data,
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