Wasn't the original question directed to our (growing) feeling that many
times PISA says No obvious oligomerization pattern but we already have
evidence of dimer formation etc..
This should happen occasionally as the approach implied in the
calculations is statistical in a sense. We should not be
On Wednesday, 31 August 2011, Jan Dohnalek wrote:
Wasn't the original question directed to our (growing) feeling that many
times PISA says No obvious oligomerization pattern but we already have
evidence of dimer formation etc..
This should happen occasionally as the approach implied in the
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
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 in a
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,
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,
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.
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 CCP4
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
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
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
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
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
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
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
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