Dear Arko,
An average B-factor of 25 does not exclude that certain atoms have
B-factors of 150 or more, as long as this is compensated by atoms with a
low B-factor (say 5-10). If you select in coot - and then click on a residue, you will get a listing of the
occupancies and temperature factors
The programme is now available for this CECAM Collaborative Scientific Software
Development meeting, sponsored by CCP4 and WeNMR.
Please register at:
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Monday 21st May Chair: Dave Stuart
1300
Simplest is to submit your current structure to PDBe - they have software
which moves all waters to lie close to protein. However the waters IDs
don't help you know if A OH 123 matches B OH 123 for example.
The very old utility water tidy tries to give meaningful names to your
waters, but those nam
Thank you Professor. Its very helpful.
Regards,Rajesh
Date: Mon, 23 Apr 2012 12:19:09 +0100
Subject: Re: [ccp4bb] finding NCS in water
From: eleanor.dod...@york.ac.uk
To: ccp4...@hotmail.com
CC: CCP4BB@jiscmail.ac.uk
Simplest is to submit your current structure to PDBe - they have software which
On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote:
> baverage program in ccp4 gave average bfactor of 25.0 for the residue
> but coot is showing 150!
Variance is the square of standard deviation, thus var=150 means
sigmaB~12 in that particular residue. High, but not impossible.
--
I do
Dear Benini,Tina, Tim, Patrick, Tom, James, Mark and other CCP4ers,
Thank you very much for your suggestions!
First, as you suggested, I already applied microseeding
(strategies: seeds vs precipitants; seeds vs drop ratio) . SeMet protein
indeed crystallized in that case, but crysta
Dear all,
I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result).
But when I used sfcheck to validate the coordinates and structure factors, I
got a high R factor > 0.38 !
Could anybody tell me the reason? Is that possible to deposit the coordinate to
PDB?
Thank you ver
Dear User of the Lujan Center,
You are invited to submit research proposals for time on the *neutron
Protein Crystallography Station* for the 2012 run cycle that begins on
August 4, 2012. This run cycle will continue through December, 2012.
Thus there will be only *one proposal call for 2012*.
*
On Mon, 2012-04-23 at 23:39 +0800, Qixu Cai wrote:
> Dear all,
>
> I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result).
> But when I used sfcheck to validate the coordinates and structure factors, I
> got a high R factor > 0.38 !
>
> Could anybody tell me the reason? I
BBers,
In my new 6.2.0 installation I'm getting "child killed: segmentation violation"
while running Truncate. The /tmp/Vaheh directory does exist and is writable.
Below is the message:
[Vaheh] ===
The program run with command: /usr/bin/ccp4-6.2.0/bin/ctru
Dear Ed,
Why the variance is the square of standard deviation?
thank you very much!
在 2012年4月23日，20:53，Ed Pozharski 写道：
> On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote:
>> baverage program in ccp4 gave average bfactor of 25.0 for the residue
>> but coot is showing 150!
>
> Varia
Dear All;
This is a sort of naive question about the NI-NTA affinity purification.
Is the Ni-NTA column from GE health able to capture proteins at 0.2ug/ml
to 0.5ug/ml?
IF not, then it is necessary to concentrate the mammalian expression
supernatant.
Thank
Hi,
At such concentrations, it might be necessary to concentrate the medium.
Otherwise you are likely to be working well below the KD of the affinity beads.
At 0.5mg/L, 50KDalton gives you 10nM. The KD of Ni-NTA should be around 1uM,
according to published SPR data
http://www.sciencedirect.co
Dear Johan,
"the standard deviation is defined as the square root of the variance." while "The
standard deviation has the same unit as the values you're measuring."
So we can say what's the unit of deviation? Is it the square of the unit of
standard deviation?
I always think that the unit of
Dear Crystallographers,
We have obtained a 1.7 A dataset for a crystal harvested from crystallization
drop after 2 weeks of soaking with inhibitor. The inhibitor has an aromatic
ring and also an acidic tail derived from other known inhibitors. The active
site hydrophobic crown had been reporte
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