Hi Robbie,
I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be avoided
? (I guess we all know we should never bias Rfree!)
> My point was that we normally do not calculate R-free after real-space
> refinement,
It's
Dear Herman
On 24 April 2014 22:32, wrote:
>
>
> The X-ray coherent length is depending on the crystal, not the synchrotron
> and my gut feeling is that it is at least several hundred unit cells, but
> here other experts may correct me.
>
>
>
I assume you meant that the coherence length is a pr
There are two kinds of "coherence length": transverse and longitudinal.
Longitudinal coherence is often quoted as delta-lambda/lambda, which is
easy to calculate but unfortunately completely irrelevant for diffraction
from crystals. If it weren't then Laue diffraction wouldn't produce spots.
Tran
Dear Chen,
Twinning can be thought of as of two or more macro-crystals glued or grown
together. The reason that the reflections often overlap is that they share one
common plane from which they grow in different directions. Many twinning tests
are based on the fact that the two (or more) macro
Eugene,
SBGrid Consortium supports certain paid programs such as Pymol, Schrodinger,
and Geneious, and academic laboratories have access to a limited pool of
tokens. For more serious computations it might be easier to get an individual
license, yet for starters the SBGrid shared-token library i
Hi Xiaoming,
I would download pdb2pqr 1.8 from the apbs website and install it.
(linux)
It can handle nucleic acid, (3 letter code) .
After you installed it run it with
python /whereeveritis/pdb2pqr-1.8/pdb2pqr.py -h
it will print the options.
Hope this helps.
Fred
[32m
Hi Xiaoming,
I don't have the pdb2pqr manual in front of me right now. In cases where the pdb2pqr instructions don't address the problem that I faced I sent a message to their BB. They always came up with a solution. Just try to send them a message.
Boaz
Boaz Shaanan, Ph.D.
Dear all,
Hello! I am kinda confused and am thinking about the definition of twinning
and disorder. I am just a starting student and might make some fundamental
mistakes.
1) Twinning is a macroscopic phenomenon and the result is the addition of
the intensity from different lattices; disorder is
Hi Boaz:
I tried running pdb2pqr server online, but it ended up with an error,
saying "local variable 'key' referenced before assignment", which I don't
know how to understand and handle with.
Thanks,
Xiaoming
On Thu, Apr 24, 2014 at 3:59 PM, Boaz Shaanan wrote:
> Hi,
>
> It's pdb2pqr problem
Hi,
It's pdb2pqr problem (unknown residue). I guess you ran pdb2pqr prior to
running APBS, if not, you should. So, you should submit your question to either
the APBS or pdb2pqr BB's. They are very helpful people.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-G
Dear all:
I'm having a problem create the electrostatic surface for a DNA chain
containing several modified nucleotides. APBS could not identify those residues
and reported them as unassigned.
What should I do to solve this problem?
Thanks a lot and best,
Xiaoming
Hi Pavel,
I agree that you bias R-free after the real-space refinement and a
quantification would be very interesting. My point was that we normally do not
calculate R-free after real-space refinement, but after reciprocal space
refinement. Here the bias is removed again. So, the problem with b
Hi Pavel
When you say "I can clearly demonstrate it", does "it" refer to the fact
that Rfree gets biased? Have you explored how strong the effect is?
To date, I'd laboured under the impression that real and reciprocal
space are numerically very different things, i.e. what you refer to as
"m
Dear Petr Leiman :
It could be the result of series termination in anomolous map.(not sure)
The error in the position results in a shifted position in the 2Fo-Fc map.
As a check it is worthwhile to see an average of the two positions (three
coordinates) results in a feature consistent with Bijvo
Dear all,
Applications are invited for an EPSRC CASE award in membrane protein
crystallography and electron microscopy.
This PhD, funded by Pfizer Neusentis and an EPSRC CASE award, will use a
multidisciplinary approach to study membrane ion channels important for human
health and disease. T
Hi Robbie,
I agree with Ed that you probably should not leave out your free
> reflections in real-space under normal circumstances.
>
Phoebe is right: you should not use free-r reflections in calculation of
map that you are going to use for real-space refinement. Otherwise you will
be biasing Rfr
Hi Phoebe,
I agree with Ed that you probably should not leave out your free reflections in
real-space under normal circumstances. Especially the low resolution
reflections will make your map look bad if set to 0.
Anyway, if real-space refinement is followed by reciprocal space refinement,
and
i.e. if you omit the free reflections, instead of biasing them toward
the measurements and giving an unrealistically low R-free, you would be biasing
them toward zero and giving an unrealistically high R-free.
However that problem might be largely alleviated by omitting the free
reflections
but u
On 04/24/2014 08:33 AM, Phoebe A. Rice wrote:
> If you are doing real-space refinement of the entire model against a map in
> coot, isn't it also important to make sure that the Rfree reflections were
> NOT used in calculating that map? Depending on how the map was made, that
> info can be hidd
Dear Jason,
thank you so much for you deep commitment and your invaluable contributions to
PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed
to give it a new home at Schrödinger. We are sorry to see you leave and will
truly miss you here.
To me personally, you hav
PLEASE do NOT do MR - You will most likely finish up with a different
origin for your SG, and it will make comparisons a pain in the neck!
Just do a rigid body refinement starting with the native structure. If you
like you can change the cell to the substrate one
pdbset xyzin native.pdb xyzout su
If you are doing real-space refinement of the entire model against a map in
coot, isn't it also important to make sure that the Rfree reflections were NOT
used in calculating that map? Depending on how the map was made, that info can
be hidden in the fine print.
+++
We would like to remind students that it one week to the application
deadline (1st May) for the BCA/CCP4 Summer School in Protein
Crystallography to be held at Diamond (UK) from Tuesday 26th August to
Sunday 31st August 2014.
We would also like to remind referees that references are due by 8th
I would do a rigid body refinement, rebuild the structure and then go on with
refinement. To compare refined structures, you still need to superimpose them
first.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Faisal
Tarique
Gesendet: Donnerstag, 24. April 2
Dear all
I have a high resolution (2A) native structure of a protein and structure
factors for a relatively low resolution (2.6A) of the same protein bound
with its substrate (complex) having same space group and cell parameters
(P212121 is the space group and cell parameters are a,b,c =39.4,64.5,
Hi Petr,
A few thoughts:
1) The Bijvoet difference Fourier is an approximation to the true imaginary
part of the electron density, and because of this shifts in the positions
of peaks in this map relative to the 2Fo-Fc map might be expected. This is
described in Hendrickson et al. Acta Cryst A43
> SBGrid is a also good option if you can afford it. It comes with PyMOL
> licenses.
- it would be helpful if SBGrid people can comment on this. AFAIK, nothing in
SBGrid comes with paid licenses, and SBGrid fees are just for installing and
maintaining the software. Individual program licenses a
A technecality - the Dano only contains information about anomalous
scatterers and should therefore show these more precisely.
The 2Fo-Fc map will tend to show anything which is included in the phasing
at the position given.
For safety you can set all the atom occupancies in the vicinity of the
Dear All,
We are looking for an explanation for a very strange observation.
Problem:
We have two fully independent data sets (two different crystals), in which the
Bijvoet Difference Fourier map peak of one particular metal site is shifted by
0.47 A from its position in the 2Fo-Fc map.
Relevan
Hi all,
I don't know why my posting about validation reports re-appeared several
times. The mail headers show that all 4 came through the domain ouhsc.edu but
why they would be resent to ccp4bb is not clear, nor why this only happened
with my posting.
--Gerard
This was resolved off-line, but in case anyone else has similar problems with
Phaser or any other program launched from ccp4i, it’s probably worth sharing
this with the rest of the BB.
We worked out that there was no way the Phaser interface distributed with
ccp4-6.4.0 could generate the “PACK
31 matches
Mail list logo
