Just for the record, except for charge density studies most small molecule
structures are refined with neutral atom scattering factors even when ions such
as Cl- are present. For example SHELX uses "4 Gaussian plus const:
International
Tables for Crystallography (1992)". Users rarely input ionic
Dear all,
Just as a historic reminder, I feel necessary to mention a key article on
refinement, written by R.Aragwal (1978) in Acta Cryst A, where he used 1- and
2-gaussian atomic factors (obviously, less precise that 4 gaussians + constant
but allowed him at that moment to accelerate as much a
James - you are fantastic!
This is so educational..
Eleanor
On 11/02/2011 02:36 AM, James Holton wrote:
On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin wrote:
Does that mean, that with Bf>10 we cannot distinguish Mg and water by electron
density peak profile? Even if oxygen in water has twice
James, this doesn't take the effect of resolution cut-offs into
account, right? You appear to be assuming that you have data to
atomic resolution (~ 1 A) or better. The integral of the scattering
factor should be confined to the experimental resolution range,
otherwise it's not going to be very r
does not seem to create anything "runnable" - please any experience here?
I downloaded the latest Windows package "all users" - type. Installed under
admin (as it would not let me otherwise).
Now as a user I cannot start the interface no matter what I try. There is
no ccp4.setup file ...
Jan
--
Dear all
Does anyone know what tools can get a topology diagram ? Thanks!
Zhang Qi
lysudiezhang1985 via foxmail
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Dear Zhang Qi,
I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein
which quickly takes you to e.g. pdbsum.
Tim
On 11/03/2011 01:48 PM, lysudiezhang1985 wrote:
> Dear all
>
> Does anyone know what tools can get a topology diagram ? T
Hmm, works fine for me. Maybe disable user account control?
Jacob
On Thu, Nov 3, 2011 at 7:54 AM, Jan Dohnalek wrote:
> does not seem to create anything "runnable" - please any experience here?
>
> I downloaded the latest Windows package "all users" - type. Installed under
> admin (as it would n
I have slightly different problem. I have windows 7 Enterprise. I don't get any
shortcuts on my desktop after installation.I work with admin account. If I try
to execute /ccp4-6.2.0/ccp4i/bin/ccp4i.tcl I get the following error. please
see attachment.I installed " ActiveTcl8.4.19.5.294332-win32
Yes, in my gnuplot "form factor" functions, "x" is the real-space
distance from the center of the atom in Angstrom and the "return value"
is electron density in electrons/A^3.
I did not realize the gnuplot file would be so interesting! If anyone
wants the reciprocal-space version (which is si
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
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
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
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
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
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
That lmgtfy.com is as almost as cool as HHpred.
Thanks for a very useful piece of information!
Petr
On Nov 3, 2011, at 2:06 PM, Tim Gruene wrote:
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>
> Dear Zhang Qi,
>
> I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein
> whi
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