We wish to recruit a Research Associate to work in the research group of
Professor Xiaodong Zhang (www.msf.bio.ic.ac.ukhttp://www.msf.bio.ac.uk), in
the Section of Structural Biology, Department of Medicine, at Imperial College
London’s South Kensington Campus. The successful candidate will
Dear Lu Zuokun,
since you can use the output mtz-file from ArpWarp for model building,
but not for refinement, there is no need to include the Rfree flag in
its output file. Maybe the omission is a deliberate caveat to the users
to pay attention to this.
Best regards,
Tim
On 10/20/2014 04:41
Hello everyone,
I would like to take a advice from you all. I have protein like 200 KDa
when i lode in a gel it shows band on 200KDa, Is that this protein gets
dimer or anything else is happening.
I would appreciate for some open discussion.
--
* Regards,** Arun *
Well,
If it is an SDS-PAGE gel, then the act of boiling the protein in detergent
generally denatures the protein and breaks apart non-covalent interactions.
To assess dimerisation, a non-denaturing technique might be more helpful.
Native-PAGE, Size Exlusion Chromatography, Analytical
Dear Colin and Tim,
But ARPwARP uses REFMAC5 for refinement, does this means that REFMAC5 uses
all reflections as working set?
How to validate that the refinement is not over fit?
Best wishes!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
At 2014-10-20 17:38:58, Tim Gruene
Hi all,
I tried using mapsig for the first time, and I got multiple errors (text
pasted at bottom). This is on mac os x 10.8.5, and the CCP4 install is
6.4.0. I followed these instructions to be able to use CCP4 programs at the
command line:
When you chose the option “Do not use the Free R flag”, then you were telling
Refmac not to use cross-validation and therefore to use all reflections as the
working set.
My experience (doubtless very limited compared to the ARP/wARP developers) is
that it’s significantly better to use the
Please ignore my incredibly dumb last email… autocomplete had me putting in
.pdb files, which obviously won't work.
Scott
On Mon, Oct 20, 2014 at 9:47 AM, Scott Horowitz horow...@umich.edu wrote:
Hi all,
I tried using mapsig for the first time, and I got multiple errors (text
pasted at
Dear Lu Zuokun,
The option you mention do not use the Free R flag, tells ARP/wARP to do
refinement without using the R-free flags, so it does not seem strange to
me that it would output a file without those labels.
I don't know why this would be a good idea, though, if you want to continue
Hi all,
Now that I have mapsig running, I am getting an error message that I am
confused by. The maps I am using are anomalous maps generated by FFT.
Originally, I had them covering just the asymmetric unit, but based on the
error message below, I then redid it where I covered a user defined
Hi Scott, it's complaining that the input files are not in the standard
CCP4 map format. Since they have the extension 'pdb' and not 'map' could
they by any chance be PDB format files? If so then this won't work!
Cheers
-- Ian
On 20 October 2014 14:47, Scott Horowitz horow...@umich.edu wrote:
Hi Scott
Our mails crossed: you worked it out yourself a microsecond before I did!
Cheers
-- Ian
On 20 October 2014 14:54, Scott Horowitz horow...@umich.edu wrote:
Please ignore my incredibly dumb last email… autocomplete had me putting
in .pdb files, which obviously won't work.
Scott
Dear Lu,
The MTZ file produced at the end of the ARP/wARP protein model
building is created by Refmac and contains the following:
1. New columns created for the built model: (FC, PHIC, FC_ALL,
PHIC_ALL, FWT, PHWT, DELFWT, PHDELWT, FOM,
Dear CCP4 Users,
I seek your valuable advice and suggestion in carrying out the normal mode
structure refinement which manifest the dynamics of protein as linear
combination of harmonic modes, used to describe the motion of protein
structure in collective fashion. Studies suggest that it is highly
On Monday, 20 October, 2014 18:10:03 Appu kumar wrote:
Dear CCP4 Users,
I seek your valuable advice and suggestion in carrying out the normal mode
structure refinement which manifest the dynamics of protein as linear
combination of harmonic modes, used to describe the motion of protein
I agree with Ethan.
In philosophy, NMA is a useful analysis to study low frequency collective
motions. That is true by taking a stand-alone structure and explore such
motions of biological interest. Domain motions in the crystallographic
environment need not necessarily correspond to those
Hello,
You can also contact elNemo or NOMAD-Ref server developers about getting
covariance/correlation matrices from normal mode analysis outputs to know
the correctly coordinated mobile atoms. In this way you can compare with
biological data also. In Shekhar's said paper K. Suhre (one of the
17 matches
Mail list logo
