Dear ccp4ers
I just wonder whether anybody knows if the PISA software could be used/modified
to detect potential interfaces of interaction of different proteins? This would
be very useful as a tool to validate protein-protein interactions detected by
in vivo methods such as yeast 2 hybrid
Before any further attempts you must check that the crystals have the same unit
cell volume. I usually do this using matthewscoeff from the GUI
( By the way why isn't the volume automatically written into the mtz header
asap!!!)
If the cell volumes differ by as much as 5% no reindexing or any
A technical remark in relation to the CC1/2, XDS issue: Refmac currently
reports Rfactors vs. resolution shells (i.e. Rw/Rf in each resolution shell).
That is useful for one aspect of the analysis, however, in the K D paper,
it's the change in overall Rfactors vs. resolution that is
Eleanor
But is the R factor a good way to assess this? - in fact who cares if
R looks worse, the goal of structure refinement after all is certainly
not to get a better R factor! The R factor if it's anything is a
measure of comparative model quality, not comparative data quality.
What I mean is
Begin forwarded message:
From: Eleanor Dodson eleanor.dod...@york.ac.uk
Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off
Date: 8 August 2012 10:10:55 GMT+01:00
To: Marcus Fislage marcus.fisl...@vib-vub.be
Cc: CCP4BB@JISCMAIL.AC.UK
Like Ian, I tend to use as much data as is
Hi
I would like to know whether it is possible to get to know the number of
molecules (helices) present in a coiled coil based on its XRD pattern.
I only know that for coiled coil there will be a meridian arc around 5.1 A
(corresponding to helical repeat) and an equatorial arc around 10 A
While building our crystal structure model we encountered density which
we weren't able to assign. The unknown molecule/molecules seems to
coordinate a Ni^2+ -ion. This ion is also coordinated by a histidin and
probably one H_2 O-molecule. The crystals have been grown from a
protein-complex
Maybe
Nat
Protoc.http://www.ncbi.nlm.nih.gov/pubmed?term=Predicting%20protein-protein%20interactions%20on%20a%20proteome%20scale%20by%20matching%20evolutionary%20and%20structural%20similarities%20at%20interfaces%20using%20PRISM#
2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367.
All:
Joel's attempt to post an interesting article somehow got concatenated 3 times.
The URL should be:
http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615et_rid=54732139
Also in an off-board conversation,
Hi Careina
To my knowledge PISA by itself is not able to do interface prediction.
In any case there are a few methods available for protein-protein
interface prediction. See for example this nice compilation:
3 (Three) Cancer Research UK-funded Postdoctoral Research Fellow positions
are available immediately in the laboratory of Professor Laurence Pearl
FRS and Dr Antony Oliver, to study the structural basis for the assembly
and specificity of multi-protein complexes involved in the recognition and
Perhaps IBIS does what you want?
http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi
IBIS ... infers/predicts interacting partners and binding sites by homology
-- David
On 8 August 2012 07:33, Careina Edgooms careinaedgo...@yahoo.com wrote:
Dear ccp4ers
I just wonder whether anybody
Hi Careina,
I asked the exactly same question in this year's CCP4 summer school @APS,
and the answer I got was no ... PISA is not for predicting
Cheers,
Xun
Sent from my iPad
On Aug 8, 2012, at 2:33 AM, Careina Edgooms careinaedgo...@yahoo.com wrote:
Dear ccp4ers
I just
Dear Colleagues,
I would like to draw your attention on behalf of Dr. Guillermo Calero that
the 70th Annual Pittsburgh diffraction conference will be held in the
beautiful state of California this coming September. This meeting
will bring together many great speakers in the field of structural
You might be interested in some work done on NikA, which binds a nickel complex
with a small organic ligand. They tentatively identified the ligand as
butane-1,2,4-tricarboxylate.
http://www.rcsb.org/pdb/explore.do?structureId=3e3k
Good luck,
Arthur
On Aug 8, 2012, at 4:56 AM, Mario Sniady
From: Mario Sniady [mailto:mario.sni...@bph.rub.de]
Sent: Wednesday, August 08, 2012 7:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unexplainable Density
It looks like it could be citrate. Is there any possibility of that?
John Andersen
While building our crystal structure model we
It is hard for me to visualize density with just screenshots - I like
to rotate the image to see the 3d. This is really clear density, however,
and you should be able to figure out what it is. As far as I can tell
from your images it looks like half of an EDTA with the other half trailing
off
Hi all,
I was trying to get maps using the *fetch PDB and Map using EDS option* in
coot, however the map would not open I am using coot version 0.6.2 was
wondering if anybody else had similar problems and how to fix this, the
following is the error message I get. It used to work fine with a
It appears that the Electron Density Server could not calculate a map
for 3TVN. These cryptic messages are what you get from Coot when there
is no map on the server. I can see from the RCSB web page that there is
no EDS link in the Experimental Details section, which also happens
when the EDS
The 3tvn coordinates/SF were released today. I'm not sure what the lag time
is between the PDB and EDS but you'd probably need to download the
structure factors and generate the map yourself.
If you're not in a super rush I know the person who refined that specific
PDB and I may be able to get
On 08/08/12 14:31, Katherine Sippel wrote:
The 3tvn coordinates/SF were released today. I'm not sure what the lag
time is between the PDB and EDS but you'd probably need to download the
structure factors and generate the map yourself.
A very good point. I saw the deposition date of 2011
On 08/08/12 21:39, Shya Biswas wrote:
Hi all,
I was trying to get maps using the *fetch PDB and Map using EDS
option* in coot, however the map would not open I am using coot
version 0.6.2 was wondering if anybody else had similar problems and
how to fix this, the following is the error
Hi,
Thanks, I think the problem is with the EDS server as I tried numerous pdb
files (not just the 3TVN) and none of them worked so far.
Shya
On Wed, Aug 8, 2012 at 5:47 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
On 08/08/12 21:39, Shya Biswas wrote:
Hi all,
I was trying to get maps
I'm unable to reproduce the error.
Can you try it in a temporary new account that doesn't have anything modified,
and see if it works?
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of
Shya Biswas wrote:
Hi,
Thanks, I think the problem is with the EDS server as I tried numerous pdb
files (not just the 3TVN) and none of
them worked so far.
Shya
I suppose that when the first message in this thread came out yesterday morning,
it was a signal for hundreds of thousands of WW
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