I guess both of the mentioned possibilities occur and it is hard to judge
which one it is for a particular case.
PISA is extremely useful for clear-cut cases to judge them quick. In the
"borderline" ones it remains to be the task of the research teams to prove
what sort of oligomerisation state is
Dear all,
registration is currently open for the postgraduate certificate
course in Protein Crystallography via the web at Birkbeck that starts on
Monday October the 3rd. It is for the duration of 1 year during which all
aspects of protein crystallography will be covered from the fundame
This is regarding Ethan´s point, particularly:
>2) the protein has crystallized as a monomer even though it
>[sometimes] exists in solution as a dimer. The interface
>seen in the crystal is not the "real" dimer interface and
>thus the PISA score is correct.
I see the same exact interface i
I noticed this kind of thing myself a long time ago, and wondered what
refmac was doing to make things "worse", so I let it keep going. And
going and going. I was delighted to "discover" that although R and/or
Rfree could rise over up to hundreds of cycles, it almost invariably
turns around again,
Dear all,
We just upgraded to ccp4 6.2.0 and with that upgrade switched from Phaser 2.1.4
to 2.3.0. During testing we ran into the problem that for some of our datasets
phaser stops with a floating point exception . As it is not the case for all
datasets I asume it must be linked to the input m
Hi,
Could you send me some representative logfiles (probably off-list)? This might
give a hint. It must be something unusual, because we have a fairly wide range
of test cases and none of them have any problems.
Thanks and best wishes,
Randy Read
On 1 Sep 2011, at 14:58, alexander.schif...@
Dear all,
We're looking for some advice about how to proceed with a structure we're
working on. Our protein is 750 amino acids and naturally binds zinc. We have
a SeMet data set that goes down to 3.7 angstroms. 4 of 8 selenium sites are
ordered and visible in addition to our zincs and we've
I am almost sure this has been addressed before, so you can go after me
for insufficient googling. However,
1. Is there any *significant* advantage in using 64-bit CCP4 binaries
(primarily speed)?
2. IIUC, the standard CCP4 download results in 32-bit binaries being
run on a 64-bit system. Work
On Thursday, September 01, 2011 11:02:50 am Ed Pozharski wrote:
> I am almost sure this has been addressed before, so you can go after me
> for insufficient googling. However,
>
> 1. Is there any *significant* advantage in using 64-bit CCP4 binaries
> (primarily speed)?
> 2. IIUC, the standard
Hi,
Depending on how many zn sites you have, you may be able to do zn-mad
for your native crystals. You don't mention if you've tried combining
your various sources of phase information; if not, it's worth looking into.
You may also want to look into various multi-crystal techniques
(averagi
How about phase extension using DM, sure you say you only have one mol per asu
but it might still be worth trying various approaches of solvent
flattening/flipping.
Don't know what you used to detect your sites and refine them, but it also
might be worth sticking them into Sharp with your partia
In my (SHELX) experience, the difference in performance between 32bit and
64bit versions running on a 64bit OS scarcely justifies distributing two
sets of binaries. The 64bit binaries are usually slightly faster (especially
the multi-CPU SHELXD). As far as I know, there are no problems running the
Dear Crystallographers,
I recently have been working with a 2.5 Ang SeMet peak wavelength
dataset which contains 2 cys's and also a couple of bona fide Cl ions
(reasonable b-factor/site is semi-buried/water does not work). In the
FFT anomalous difference map using PhiC from the refined model and
D
Where in refinement of your model are you ?
At an early stage I wouldn't be surprised to only see SeMets but once you've
refined your structure and go back to calculate an anomalous map with the
improved phases you might double your signal for SeMet and start seeing sulfurs.
An alternative explan
Hi Jacob
I agree with Juergen, and just add that your Cys and Cl might not be
fully occupied.
cheers
Preben
On 9/1/11 10:03 PM, Jacob Keller wrote:
Dear Crystallographers,
I recently have been working with a 2.5 Ang SeMet peak wavelength
dataset which contains 2 cys's and also a couple of bon
Update:
I tried more anomalous maps, this time with the originally-deposited
data at 1.8 Ang (mine were similar, substrate-soaked crystals) and
phases from the refined model, and the Se sites are now ~40-50 sigma,
and there is still totally nothing at the Cl and S sites, even though
in 2Fo-Fc the
I'd be surprised if the model phases were introducing bias into an
anomalous difference map (they might be adding noise, but that's another
story). I've also never seen feedback in model-phased anomalous
difference maps (experimental-phased anomalous difference maps can have
pretty bad feedbac
Hi Basu,
You mentioned molecular replacement was not successful for this project. Which
model was used for this procedure? Have you tried your partially built
structure as a model to obtain preliminary phases for your native (2.7A) data
set? If there is any luck with that, you might be able to
hi all
I have crystals which have tendency to stick with the plate and while i try
to pick them for mounting on the loop they get broken.I have also tried to
tools to detach the crystals from the plate but couldnt get success. before
picking the best crystals I would like to know if someone has ex
Der Atul
this topic was previously summarized on the ccp4wiki
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals
best
Savvas
On 02 Sep 2011, at 08:00, atul kumar wrote:
> hi all
>
> I have crystals which have tendency to stick with the plate and while i try
> to pick
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