On Tue, 1 Apr 2014 17:28:48 +0200, Almudena Ponce Salvatierra
wrote:
>sorry, I missed this part of the error message:
>
>!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE PARAMETERS HAS FAILED.
> YOU MAY RESTART THIS STEP AFTER SPECIFYING VALUES IN XDS.INP
>FOR:
> RE
It means that there exists a technical problem that probably has nothing
directly to do with your data and XDS: the program tried to read data that
could not be read.
I would guess that the disk is full, or your quota exceeded.
Hope this helps,
Kay
Dear Chen,
If you don't know how many sites to expect - and in some cases, e.g. an
iodide soak, this is inevitable - I recommend trying different numbers
(FIND N in shelxd) and choosing the one where the occupancy of peak N
comes out as about 0.2. If it is higher you need a higher N and vice
This is a god example for what happens if mathematics get translated into
language. It is not a lossless transform.
1) "Rupp says a structure fator is a vector"
I hope I did not make that statement ( because it is wrong). If I explicitly
did (or that impression emerged) , it would be good to know
Encouraged by recent help from the BB in filling in gaps in my
understanding, maybe I can get help with another question:
At the top of page 121 in Blundell and Johnson, it is written:
"The total wave scattered by a small unit of volume dv at a position r relative to the
wave scattered from the
By the way, I have another question related to the number of sites. I just
rethought about what Herman mentioned, and I just realized that the number
of sites, at least strong sites, could be guessed from an anomalous
Patterson map. Therefore I looked at the anomalous Patterson of my data.
The map
Thank you very much everyone for your comments.
I will try your ideas and try to get this thing to work.
I appreciate your help
Meisam
On Mon, Mar 31, 2014 at 7:21 PM, Meisam Nosrati wrote:
> Dear CCP4ers
>
> I have crystallized a protein with a series of ligands that are not in the
> PDB.
>
Dear Jurgen,
The beam position is fine. we have collected many data sets before and
after this data. Moreover, we the Technical scientist always checks the
beam position before we mount the crystals.
Thanks
On Tue, Apr 1, 2014 at 11:23 PM, Jurgen Bosch wrote:
> check your beam position
> ..
Dear all,
I am just taking advantage of this particular thread to add my query also.
I hope you don't mind Chen.
We haven't solved any structure in our lab using SAD phasing, so pardon me
for sounding naive.
I have a 6.5 A data of anomalous scattering with a 3.5 A data using the Cu
anode.My crys
On 1 April 2014 00:12, Edward A. Berry wrote:
> Yes of course, but if you start from the left you are not (at least not
> obviously)
> "first rotating the coordinates by alpha about z"; you are rotating the
> columns
> of the second matrix. And in the second multiplication you are not
> rotating
Dear Almudena,
You can try to run XDS with 300 frames. At the end, you have to open the
file called INTEGRATE.LP and copy the refined value of
REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.=
BEAM_DIVERGENCE=BEAM_DIVERGENCE_E.S.D.=
at the end of your XDS.INP.
Now, you can re-run XDS with all
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sorry, I missed this part of the error message:
!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE PARAMETERS HAS FAILED.
YOU MAY RESTART THIS STEP AFTER SPECIFYING VALUES IN XDS.INP
FOR:
REFLECTING_RANGE=REFLECTING_RANGE_E.S.D.=
BEAM_DIVERGENCE=
Dear CCP4 users,
while I am running CORRECT within XDS, the program suddenly stops, and
gives the following message:
forrtl: severe (24): end-of-file during read, unit 2, file
/data/almudena/160314SLS/dts2/bin1_01.tmp
I actually don't know what it means. I could run it with no problems with
300
Dear Herman,
Thank you so much for your suggestions. The density that passes through the
rotational axis is so strong and extended that can be considered as a
significant portion of the molecule. However, some density in the middle
might show some features. I have no experience and this could be o
Dear all,
On April 28-29th Nature conferences, SGC and University of Campinas will
realize a workshop entitled "Chemical Probe-based Open Science: Uncovering
New Human and Plant Biology". It will be held at the University of Campinas
(Unicamp), in Campinas-São Paulo, Brazil. It is a good opportuni
Dear Chen,
I am not an expert on SAD and MAD. However, at this stage I would not worry too
much about density going through the 2-fold axis. There might be a sulfate ion
or some other buffer component present at that position, or it may just be an
artifact that will go away once the structure ha
Dear Savvas,
Thank you for your reply and your nice protocol. I am also worried of this
problem so I have already run my crystals on the gel for several times. The
result is so clean that you can hardly draw any other conclusions except
that the crystals are made up of the full-length molecule. Bu
On 1 April 2014 00:12, Edward A. Berry wrote:
> I need to work on something else now, but when i get time I will go
> through Ian's derivation and see how it is in fact tractable.
>
I should point out that it's not my derivation. This proof was given to me
by Tilman Shirmer. For the original
Dear Friends
I have a protein-peptide complex crystals, which is diffracted at 3.8
resolution with a P41212 space group. We solved the structure using
molecular replacement method, which shows that there are thre molecules in
asymmetric unit. Unfortunately one of the chain in this asymmetric un
Dear Meisam,
In the past I had similar problems, because of jligand and other cif
generators can make errors when generate cif files, as it has been
written before. I have solved these problems by using sketcher (ccp4)
and PRODRG server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg).
I u
Dear Chen,
how sure are you that your crystals contain the protein of interest? Repeatedly
washing harversted crystals in crystal stabilization solution followed by
SDS-PAGE coupled to appropriate staining protocols (e.g. Coomassie, Silver
staining) or western blotting can give a pretty conclus
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Dear Ed,
It looks like the problem is not yet closed, so I'll add my remarks.
In addition to very detailed comments by Ian, Tim and others, it might be
useful to look our article in J.Appl.Cryst (1997), 30, 402-410, which addresses
exactly these confusing points: what is rotated, what is fixed,
Dear Meisam,
For me it does work and if I import a cif dictionary it will override the
existing definition. I default use INH for the ligand name which has already
been taken by the pdb without any problems.
Assuming that you have used the correct procedure to import the cif directory
in refma
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