Agree!
I think for crystallographic use the nanodrop is perfectly okay to see if
the protein is 5mg/ml or 30mg/ml. But in fact I also do not trust our
instrument if it comes to more important issues like preparing solutions for
titrations or assays. And due to the small pathlength I do not trust
Hi Huiying,
could you tell us which version of refmac you are using?
There has been an issue with torsion definitions in ligands NEVER
included in the refinement, even if they were in the cif (at least up to
Refmac_5.2.0019). I did have the same effect you had and wondered why.
(See list in Oct
Which brings us back to the Hellma "TrayCell" solution where you can,
from the same spectrometer, have both the cuvette option and the
quickness of the NanoDrop/NanoVue system.
Anyone that can comment on the performance of the TrayCell from Hellma?
Cheers,
Martin
On Dec 5, 2008, at 9:06 AM
Hi,
What is the meaning of R free of perfect twin? Shelxl counts it but it
seems that the R f is no longer independent.
Aga
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Hash: SHA1
I guess the independence is mostly depending on how you select the
reflection that lie in the free-set.
If (from the beginning) you select reflections that are related by the
twin operator to be both in the free-set you keep the "independence"
POSTGRADUATE SCHOLARSHIP in chemistry, within the discipline of molecular
biophysics, with placement at the Department of Chemistry, Division of
Molecular Biophysics, Faculty of Science.
Reference Number: N 2008/714
Starting Date: As soon as possible
Information: University lecturer Marjolein Thu
Am 5 Dec 2008 um 13:50 hat Agnieszka Kiliszek geschrieben:
> Hi,
>
> What is the meaning of R free of perfect twin? Shelxl counts it but it
> seems that the R f is no longer independent.
>
> Aga
Dear Aga,
I also had this problem, however with Refmac5.5.
My solution was to use the CNS script
registration closes today!
http://conferences.ncl.ac.uk/BCA_BSG_Winter_2008/index.htm
--
R. J. Lewis
Professor of Structural Biology
Institute for Cell and Molecular Biosciences
Faculty of Medical Sciences Tel: +44 (0)191 222 5482
University of Newcastle Fax: +44 (0)191 2
Hello everyone,
I am looking for a modeling program that will allow me to input a sequence
alignment and coordinates of a template for 3D structure prediction of a
target molecule.
I know Modeller can do the job. Are there other web based programs that can
do the same ?
Thanks
Yes of course.
I heartily recommend 3Djigsaw - (google for it) - it's a very nice and
simple to use web service that only requires a sequence as input. If you
have a very low-homology target you may not succeed with this service but
that's not necessarily a detriment since very careful attentio
to models built on low-homology structures.
since i'm currently preparing my bioinformatics lectures for next week's
teaching, i might as well be a Besserwisser and point out that homology, much
like pregnancy and death, is a binary concept. i'm sure artem knows this and
simply mistyped "low
Is death 'for tax purposes' less or more than the other kind of death?
Also, when one is pregnant with one fetus versus multiple - is it still the
same?
But seriously, this is what happens when I try to answer a question while
trying to deal with a migraine.
Artem
-Original Message-
Fro
You might be right. I can not rule out the possibility.
By the way, is the PMS/DCPIP system fairly stable in the aerobic condition?
Mike
--- On Thu, 12/4/08, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
From: [EMAIL PROTECTED] <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb] Offtopic: FAD enzymatic ass
Is there any existing example about anybody trying to do molecular
replacement for a protein-DNA complex using any B-DNA from the pdb database.
I am wondering 1) whether it is doable 2)if it is not doable, why not?
Thanks in advance for the feedback
Dear all,
Thanks a lot for raising the issue with the not reproducibility of protein
measurement with Nanodrop. We use the instrument as a workhorse in the lab.
Indeed, recently I observed that the protein concentration suggested by
Nanodrop is sometimes differ to the usual colorimetric measuremen
The keyword script Eckhard mentioned did the job I wanted to achieve. I
created the cif file for my ligand through the Monomer Library Stetcher
and then edited torsion angle part to include the restraint for the OH
tiling angle. I am running the CCP4 Suite 6.0.2 and CCP4i 1.4.4.2.
but I still h
to models built on low-homology structures.
since i'm currently preparing my bioinformatics lectures for next week's
teaching, i might as well be a Besserwisser and point out that homology,
much like pregnancy and death, is a binary concept. i'm sure artem knows
this and simply mistyped "low
Applications are invited for a postdoctoral position at Cold Spring Harbor
Laboratory from highly enthusiastic individuals with strong interest in
conducting structural and electrophysiological approaches to solve problems
in ion channels, transporters, receptors and intramembrane enzymes involved
It would be difficult because your protein probably affects the DNA
conformation. Do you have some idea how your protein affects DNA
conformation? But I think a brute force strategy trying every piece of
DNA in the PDB as a template might work. Another approach would be to
do MR using only segments
Dear sir,
Thank you all of you for your suggestions.
Sincerely
Deb
On Fri, 05 Dec 2008 Mathews,Irimpan wrote :
>Hi Deb,
>
>You may want to try some ions (cations and anions). It may help stabilize some
>loops if they have binding sites. I usually add around 5 - 10uL to 500 uL of
>the well
Dear members,
I have a little query hare about Rpim and Rmeans. How these are used to mark
data quality, and how can one calculate it.
Thak you for your reply in advance.
Sincerely
Deb
112. Weiss MS, & Hilgenfeld R (1997) On the use of the merging R factor as a
quality indicator for X-ray data. J. Appl. Cryst. 30, 203-205.
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Debajyoti Dutta
Sent: Friday, December 05, 2008 8:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [c
In addition to the Weiss paper ...
Diederichs, K and Karplus, PA (1997). Improved R-factors for
diffraction data analysis in macromolecular crystallography. Nature
Structural Biology 4(4): 269-275.
On Dec 5, 2008, at 8:06 PM, Debajyoti Dutta wrote:
Dear members,
I have a little query h
Dear Deb,
R_meas or R_rim is a merging R-factor which is independent of the
redundancy or multiplicity of the data (hence its name), R_pim
stands for precision indicating merging R-factor. R_pim
gives you the precision of the averaged measurement, which is
the one you are actually using for struct
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