"Coot MacGyver"
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Francois Berenger
Gesendet: Dienstag, 31. August 2010 08:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Format conversion of Shelx coordinate file
Hi,
What is the motto/
Dear all,
Please could you bring this advert to the attention of any potential
candidates?
With industrialization, the production of chemicals and their introduction into
the environment has increased massively. Some of these compounds act as
endocrine disrupting chemicals (EDCs) that cause ad
Unfortunately, some crystals don't diffract at all. You may want to try
to 100% verify that it's protein either by SDS-PAGE or mass-spec
(100x100x100 micron crystal could contain ~0.5mcg of protein, so you my
need to use silver staining). If it is, I'd consider trying to get
diffracting crystals
Dear All,
sorry to bother you with this but I just can't figure out what goes wrong ...
I am running the latest version of snow leopard on a MBP unibody with the 64bit
kernel.
I have an up to date fink installation for native 64bit.
With this I have installed ccp4 via fink. I have also insta
Position Available: Protein Crystallography
We have an opening for permanent position in the area of
crystallography. The position is at the Slough, UK research hub of UCB,
a leader in medicines for epilepsy and inflammatory disease. Applicants
are expected to have experience in sub-cloning, pr
Or might be worth going back to the drawing board to design more
constructs (and check them around the same conditions), thermostable
homologs etc.. what about reductive methylation, anyone had luck with
membrane proteins?
tommi
Quoting "Ed Pozharski" :
Unfortunately, some crystals don't
Well said. I've seen three cases by now when switching to a homologue
from a different organism led to solving a structure (and way too many
cases when crystals just did not diffract, either at all or well
enough :).
On Tue, 2010-08-31 at 18:48 +0300, Tommi Kajander wrote:
> Or might be worth goi
I have to say that in my limited experience with membrane protein
crystallization, these liquid crystal / spherulite type things are very
common, and seldom turn into anything useful. Perhaps others on the list
more experienced than I can corroborate or refute this. I just don't want
this guy to ge
On Tue, 2010-08-31 at 11:57 -0500, Jacob Keller wrote:
> I just don't want this guy to get misled into perhaps wasting
> months/years on something not particularly promising.
Trouble is, of course, that one never knows if a particular trick will
work this time. We routinely get PEG/fluoride salt
Hi,
I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In
the SIGMAA documentation, it says WCMB is the figure of merit; however, I
opened in coot with "FP PHIC WCMB" combination, and for lots of systems, I
didn't see too much difference against "FP PHIC" maps. Is the differenc
Hi Hailiang,
m is typically determined per resolution bin using test reflections and
it can range from 0 to 1, so the difference between corresponding mFo
and Fo can range accordingly.
You can read more on this, for example:
Acta Cryst. A42 (1986) 140-149.
Acta Cryst. (1995). A51, 880-887.
J
Hello Qiangmin,
Here are links to a few web resources that have tips for membrane protein
crystallization that may help with your optimization strategy:
http://kb.psi-structuralgenomics.org/update/2009/06/full/th_psisgkb.2009.25.html
http://web.emeraldbiosystems.com/blog/bid/33916/8-Practical-
On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote:
> Is the difference
> between mFo and Fo maps supposed to be very small?
For an essentially correct model, yes. The major advantage of (2mFo-DFc)
maps is suppression of model bias, so if you don't see much difference
then your model is very
Actually I cut a small domain from the well-defined structure (just for a
test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo
maps, and the mFo and Fo maps are so close so that I wonder whether figure
of merit generated by SIGMAA helps or not in this situation...
Best Regards
Hi,
The picture looks like detergent crystals, specially DDM crystals. I have same
crystals in many conditions.
With regards,
Parveen
Yea, Parveen has actually asked about this here a year ago and I found this
discussion quite useful indeed:
www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11717.html
and I think we all get tons of these crystals especially in conditions with
PEGs.
There are lots of things you can try and have been
If I understand correctly, the only difference between "mFo" and "Fo"
map will be weighting in different resolution shells according to
figure-of-merit. While this will presumably downweigh the less reliable
resolution shells, it will hardly make up for the heavy model bias. The
reason you see th
I have had a lot of problems of my own with poorly diffracting (or not at all)
membrane protein crystals. After a previous discussion here, I summarised the
suggestions I got in this ccp4 user wiki;
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality
There are
Remember you need to look at half the contour height in a mFo map
compared to a 2mFo-DFc map - the same domain should show up but at a
lower relative contour level in both maps.
REFMAC calculates a similar WCNG and you can look at the graph of m
after refinement to see how close it is to 1. If
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