wow this is crazy you should look into this
http://www.nb15news.net/biz/?read=6911838
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Hi Uma,
Altering sigma affects the strength of geometry restraints throughout the model
- bonds, angles, etc. Choosing a very low sigma will cause geometry to be more
tightly restrained towards "ideal" values, which is why you observe
improvements in Coot validation. Note that strengthening th
Thank you for all your suggestions.
Rigaku have discovered that shorting a couple of the output leads together
means the new type can be used as a replacement for the old type.
I'm very happy to say that it works!
This is a similar solution to that suggested by Herman Schreuder.
Kevin Roberts
It all will depend on the resolution. At low resolution, relaxing the geometric
restraints will allow the refinement program to tweak the model such that the
difference between Fobs and Fcalc is minimized, but not that the model gets
closer to the "truth". I once struggled for a long time with a
have a look at this case, no danger of your coordinates going to anyone but
yourself if you do it this way:
http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers
On 26 Apr 2012, at 12:02, Jrh wrote:
> Dear Colleagues,
> I have followed this thread with great i
Hi Uma,
The optimal weight is indeed resolution dependent, but hard to predict. In
Refmac you can follow LLfree when you optimize the restraint weight and also
keep an eye on the gap between R and R-free (it should not be too wide). Like
Rob said, your geometry should be 'reasonable'. This ma
Just in case you are blocking with BSA, how about, e. coli
beta-galactosidase (114 KDa) ?. It's commercially available but you
probably have cells already making it in the lab
On 26 April 2012 19:29, Peter Hsu wrote:
> Hi all,
>
> Sorry for the very off topic problem. I'm looking for a loading
Two points.
1) the fit to ideal geometry as flagged in coot validation does not
guarantee a correct model - the best model should be the one that fits the
experimental data best, without having unlikely geometry. You could easily
get a model with perfect geometry which was incorrectly placed in the
What I would do - not net ideal!
1) the ASP looks in the wrong place - shift it into green density and one
OE is probably a water..
2) MET notoriously hard to model - I suspect there often are multiple
conformations.. And of course at some wave lengths the S contribution
should be down weighted by
Hi,
Could someone explain to me the scientific details of the protocols used
in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and
(2) optimize their positions?
Many thanks in advance.
Greetings,
Nadir
--
Pr. Nadir T. Mrabet
Structural& Molecular Biochemistry
I
Hongjun,
I am in agreement with Bert as DDM is exceedingly difficult to crystallize,
even in organic solvents. This is one of the reasons it is so expensive.
However, you can produce a lot of "quasi"-crystals that do show low resolution
diffraction. As Bert said, you may have protein/deterge
Hi All,
Does any one add protease inhibitor to purified protein just before setting
trays?
If yes what is the typical % that should be added ?
regards
rashmi
Dear All:
Thank you very much for you comments and advices.
Now I have a better understanding on this issue.
regards
Ros
On Fri, Apr 27, 2012 at 9:25 AM, Eleanor Dodson
wrote:
> Two points.
> 1) the fit to ideal geometry as flagged in coot validation does not
> guarantee a correct model - the
Wouldn't the lack of solubility of the alpha form of DDM suggest an easy
purification protocol for the beta form?
JPK
On Fri, Apr 27, 2012 at 8:40 AM, R. M. Garavito wrote:
> Hongjun,
>
> I am in agreement with Bert as DDM is exceedingly difficult to
> crystallize, even in organic solvents. Thi
Nadir,
There is an explicit bulletin board for questions regarding CNS and XPLOR. I
would suggest posting your question there.
http://tech.dir.groups.yahoo.com/group/cnsbb/
Cheers,
Francisco
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir
Jacob,
The solubility of the alpha anomer of DDM is actually not bad (it's only really
bad for the alkyl glucosides), just the phase behavior is different. Still
getting pure beta anomer is the tough problem, which is part of the reason it
is so expensive.
Michael
***
Dear All,
With my most recent PDBe deposition, in addition to the native data, I
had intended to deposit the anomalous data, used for structure
determination, and make it available for download. This turned out to
be less straightforward than I had anticipated, because the current
PDB con
again, it looks like this is particular to the US portal.
We submit via the European www.pdbe.org and can submit multiple datasets.
See 2XGF for an example.
Note: I think from www.rcsb.org only one file can be downloaded, but
www.pdbe.org clearly shows both.
Although you are in the US, you can use
Dear Mark,
This is interesting. I also had submitted my data via the PDBe
(European portal). While they allow deposition of multiple datasets,
only a single file can apparently be made available for download from
the site. In contrast to your case, for my deposition the second
deposited d
On Friday, April 27, 2012 11:23:13 am Florian Schmitzberger wrote:
> Dear All,
>
> With my most recent PDBe deposition, in addition to the native data, I
> had intended to deposit the anomalous data, used for structure
> determination, and make it available for download. This turned out to
>
It might be a portal issue. But the pdb staff is very helpful in getting
this deposited. We deposited data of I think 4 "crystals" and 3
wavelengths with different phase sets in 2008. (The data was
anisotropic, 3.5/4.2 A resolution, model building was not straight
forward, so we wanted to preserve
All,
For those who still don't use Coot is there an automatic water picking
procedure in CCP4?
Many years ago there was a peakmax which is now for Patterson peaks only. Then
there was routine through Arp/wArp. Now is Coot only. Is this right?
Thanks.
Vaheh Oganesyan, PhD
Antibody Discovery a
Dear crystallographers
A very basic question, for anisotropic diffraction, does data truncation with
ellipsoidal method change the symmetry? For example, if untruncated data is
space group P6, will truncated data index as P622 or P2?
Thank you.
Theresa
Anisotropic truncation should have no effect on the space group symmetry.
On 04/27/12 15:18, Theresa Hsu wrote:
Dear crystallographers
A very basic question, for anisotropic diffraction, does data truncation with
ellipsoidal method change the symmetry? For example, if untruncated data is
spa
We (JCSG) too have been depositing multiple data sets (including unmerged
original index intensities for each wavelength and even for multiple crystals
when one was used for phasing and another for refinement, and MAD phases
and DM modified map coefficients) since 2004 without problems. These
ar
so perhaps the problem indeed is sending different wavelengths as one
file...in our case there is only one crystal, one wavelength, i.e. one
loop, while I clearly submitted all three wavelengths.
Quoting "Miller, Mitchell D.":
We (JCSG) too have been depositing multiple data sets (includi
The 42nd Mid-Atlantic Macromolecular Crystallography meeting will be held at
the University of Virginia from May 31 June 2, 2012. There are several
reasons why you should make your plans now! Most of the blocks of hotel rooms
will be released to the public and conference rates will expire o
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Dear ,
according to my 'man watpeak' and 'man peakmax' in ccp4-6.2.993 there
is no restrictionof these programs to Patterson peaks (which would
anyhow require a total rewrite, considering that peakmax acts on maps
rather than Pattersion maps).
May
Birtley and Curry used a novel optimization method, in their paper
"Crystallization of foot-and-mouth disease virus 3C protease: surface
mutagenesis and a novel crystal-optimization strategy", which might be
inspiring for you.
在 2012年4月28日 上午3:21，David Schuller 写道：
> Anisotropic truncation shou
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