On 7 Nov 2012, at 19:49, Jacob Keller wrote:
> Dear Crystallographers,
>
> does anyone have a script on hand which can:
>
> -read in a tab-delimited dataset
> -determine whether each row in column X is above or below some input cutoff
> value Y,
> -outputs all such rows to a new file?
>
> if
Dear Crystallographers,
does anyone have a script on hand which can:
-read in a tab-delimited dataset
-determine whether each row in column X is above or below some input cutoff
value Y,
-outputs all such rows to a new file?
if someone already has this on hand, I would appreciate it--seems like
On Wed, Nov 7, 2012 at 4:02 PM, Meisam Nosrati wrote:
> I want to know what is considered an acceptable Clash Score for a solved
> structure.
The recommendation from MolProbity is less than 10. If you have
low-resolution data and don't have a high-resolution starting model,
it could be a little
Dear CCP4ers
I want to know what is considered an acceptable Clash Score for a solved
structure.
Thanks
Meisam
Well, galvanised iron is an old story of Zn in insuline… :-\
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: +
As a follow up to Roger's statement if you are doing any sort of analytical
metal analysis be careful with the controls (metal-free water/acid washed
glassware). Also most AC/heating systems include galvanized steel in the
duct work that spits out Zn like crazy and can screw up your measurements.
I
As far as sigma level is concerned, and if I remember that you are working at
3.4 angstrom resolution - this 6 sigma is VERY STRONG.
I am sure it is a metal atom. But you can re-process your data preserving
anomalous signal and calcule anomalous map easily done in
PHENIX, less so in CCP4 and th
Actually, the symmetry relating these solutions is a 2-fold around the y-axis,
which is not a crystallographic operator in P41. So either this is a twinned
crystal, and the two solutions relate to the two twin components, or the true
symmetry is higher.
What is special about the solutions is
Tryptone and/or yeast extract is loaded with metals, including zinc. It
is almost impossible to keep zinc contamination at bay without using
carefully defined media and taking heroic measures. (I know this because
of the difficulty of making overexpressed metallo-substituted
zinc-enzymes when t
> Thanks for the heads-up. Bernhard and I have fixed several of these
> window-order problems, but this one slipped by us (neither of us use a Mac
> :-).
>
> Fixed in 0.7.1
That's great news, Paul. Thank you for fixing it and others for pointing it
out. I've been always quite convinced that it w
On 30/10/12 15:32, Eike Schulz wrote:
Dear Coot-users,
I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package
was no problem at all it runs very smoothly.
However, whenever I want to save the coordinates the saving dialog open
-behind- the main window. To be more precise:
On Wed, 2012-11-07 at 11:29 -0600, SD Y wrote:
> https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png
Your sigma level of 6.5 seems a bit low, so maybe it is a different
metal. But on your main question - yes, metal binding proteins do pick
up metals from the media. Once metal is coord
I've seen this effect too. In the case I saw the drops were growing (and
spreading) due to a reverse diffusion gradient. Optimised conditions used
"salting in" method i.e. crystallising as the [pptnt] decreases during
equilibration due to dilution as water is Tx from well to drop. Rare but not
Dear Rui,
If your search model is itself a homodimer, you expect to find 2
equivalent solution
And indeed in your case:
50.3 + 128.6 = 178.3 (= aboput 180)
0.2 + 179.8 = 180
219.8 - 38.7 = 181.1 (= about 180)
indicating that both solutions are crystallographically equivalent.
What does worry
Dear all,
I have a related question to the one I have posted "low resolution and SG", on
which I am still working based on the suggestions I have got.
The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 cys
and 1 His residues. They have add Zn in to their experiment
Hi, Dear group,
I recently collected a dataset about 2.5 A and integrated with P4. When I
tried phaser I got a sol file looks like this, is this real solution? Is
LLG high enough?
SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217
On Wed, 2012-11-07 at 16:04 +0200, Eva Bligt-Lindén wrote:
> To my knowledge the protein is not a
> surface-tension-reducing-protein and there is no detergent in the
> sample.
However your observations indicate that your sample has reduced surface
tension. When you say that "to your knowledg
Eva
Yes batch under oil will solve the problem. We regularly used to
crystallize conditions with high levels of MPD under oil without difficulty.
I agree that the protein might be reducing the surface tension, but I've
never heard of such a strong effect. Maybe the protein is unstable and
"want
Dear Eva,
are you using siliconized cover slips or normal ones ? Protein drops on not
siliconized glass tend to spread especially if they contain alcohol or
detergent. But this shouldn't be a problem with sitting drops usually.
Good luck !
Ulrike
Those are the EasyXtal 15 well tools with the EasyXtal DG-Crystal Supports.
Look at this link to find them:
http://www.qiagen.com/products/protein/crystallization/default.aspx
I agree that they keep the drops from spreading out, but I have experienced
trouble harvesting smaller crystals from
Qiagen used to sell hanging-drop trays with screw-cap tops, and the tops
had six rings on them (3 large, 3 small). The rings had a lip on them that
kept the drop from spreading beyond the edge. I found these quite useful
when setting up drops that had detergent in them.
I unfortunately don't kno
Thank you for your replies. To my knowledge the protein is not a
surface-tension-reducing-protein and there is no detergent in the
sample. I have tried different plates and still the same result. I
will try a different crystallization technique such as batch under oil
or counter-diffusion i
Hi Jim,
I remember the same discussion somectime ago on the bb. The consensus
was that there is a standard IATA document (IATA special provision A152)
for these kinds of shipments, this greatly decreases the risk of
destruction of you samples at Customs. See this thread
http://www.mail-archiv
Why don't you try batch under oil?
2012/11/7 Eva Bligt-Lindén
> Dear ccp4 users,
>
> I have a problem in the crystallization of my target protein. Whenever I
> set up a vapour diffusion experiment, either hanging or sitting drops, the
> drops spread out. The surface tension is completely lost in
Hi Frank,
I like your letter with the random initiative :-)
And then the thread by citing a regulation, which they probably never have
heard of. I would additionally add the regulation numbers for the dewar. There
are two or three IATA numbers that should be mentioned to indicate its in line
wi
Hi there,
You could try to go for liquid-liquid interface crystallisation (in
capillaries). The minimum volume would be no less than 1.5 microl
protein + 1.5 microl precipitant, i.e. not the volumes used by nanodrop
robots. Crystallisation under oil (or similar liquids) should also have
the
is your protein a STRP (surface-tension-reducing protein)?
Seriously, did you try different plates? Old-fashioned siliconised cover slips
on Linbro plates?
Does your sample contain detergent?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia
Dear ccp4 users,
I have a problem in the crystallization of my target protein. Whenever
I set up a vapour diffusion experiment, either hanging or sitting
drops, the drops spread out. The surface tension is completely lost in
80-90% of the droplets. Have any one experienced something similar
Dear CCP4
Thank you for all your suggestions regarding my problem and will try all your
ideas that were offered
best regards
Rana
Dear Jim,
For the transport of crystals in dewar, I would also write "samples" and
definitely avoid using the word "crystals" which will probably immediately
attract attention and lead to the question: "How expensive are these
crystals ?"..
Best
Christophe
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