Hi Matt,
What I want is the density 'inside' each atom in the map, so that I can make
> quantitative comparisons of "how much stuff" is present in a blob (modeled
> or not).
>
that's still ambiguous...: 1) do you want a density value calculated at a
point, which may be, for example, a center for
On Mon, May 2, 2011 at 2:18 PM, James M Holton wrote:
> The CCP4 program that makes the "label map" you are looking for is SFALL.
> It can be told to make a .map file where each grid point is still a
> floating-point number, but instead of the usual electron density it
> "encodes" the residue num
On Mon, May 2, 2011 at 12:53 PM, Pavel Afonine wrote:
> Hi Matt,
>
>
> I'm trying to 'measure' the density in a region of my structure by
>> integrating the electron density there (notwithstanding errors in F000). I
>> understand that both overlapmap and phenix.real_space_correlation compute
>>
The CCP4 program that makes the "label map" you are looking for is SFALL. It
can be told to make a .map file where each grid point is still a floating-point
number, but instead of the usual electron density it "encodes" the residue
number, atom number, etc. The OVERLAPMAP program knows how to de
Hi Matt,
I'm trying to 'measure' the density in a region of my structure by
> integrating the electron density there (notwithstanding errors in F000). I
> understand that both overlapmap and phenix.real_space_correlation compute
> density surrounding individual atoms for their calculations. Is
Hi all
I'm trying to 'measure' the density in a region of my structure by
integrating the electron density there (notwithstanding errors in F000). I
understand that both overlapmap and phenix.real_space_correlation compute
density surrounding individual atoms for their calculations. Is there any
Dear George,
Thanks for your effort. That will be of great help!
Please let us know about the new version of SHELXL when
launched.
All the best,
Fátima
Em Mon, 2 May 2011 17:12:34 +0200
"George M. Sheldrick"
escreveu:
Dear Fatima,
Thanks. I am anyway planning to allow chain identifier
Dear Fatima,
Thanks. I am anyway planning to allow chain identifiers in the next
version of SHELXL.
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22
Dear George,
I really appreciate your kind offer but I have just solved
the problem.
To all that may have the same issue in the future, I
should say that in my case the problem was related to the
use of SHELXPRO. I was not using it properly to transform
the chains read by SHELXL (numbered)
Anita,
Proteolysis and oxydation are the most common alteration affecting proteins
during the course of crystallization.
If you have drops of the trays that yielded crystals I would run a gel on
those drops and look at the aspect of protein still around in the drop. That
would give you some clues.
On Mon, 2011-05-02 at 15:48 +0800, anita p wrote:
> What are the reasons behind nonreproducibility of protein crystals?
There are many possible reasons. You could start by checking you
protein stock for signs of degradation and preparing it afresh.
--
"Hurry up before we all come back to our se
Dear Crystallographers,
I have got my protein crystallized once and then it is not reproducing,
though I am using the same batch of protein and same condition.
What are the reasons behind nonreproducibility of protein crystals?
I am very new to this field hence I apologize if it is a lame questi
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