Hi
The low pH and its interaction with PIP1 can be conflicting. The low
pH can modify the interaction site.
Nevertheless, one good way to study protein stability is thermal shift assay.
You can read this publication too : PubMed ID 16604423. (Rapid
determination of protein solubility and stability
I think the answer to your question depends on why the data is
incomplete.
James
On Mar 17, 2008, at 3:06 AM, Melody Lin wrote:
Hi all,
I have always been wondering... for a data set diffracting to say
2.15 Angstrom but in the highest resolution shell (2.25-2.15) the
completeness is 74%
Hi all,
I have always been wondering... for a data set diffracting to say
2.15Angstrom but in the highest resolution shell (
2.25-2.15) the completeness is 74%, should I use merge all the data and call
it a 2.15 A dataset or I should cut the data set to say 2.25 A where the
highest resolution shel
Hi Melody,
There was a nice discussion in this year's ccp4 study weekend. In
general, one needs to consider several factors.. If you were at 3A, or
low symmetry, you would of course try to get the maximum out of it, on
the other hand, there are requirements for experimental phasing.. in
general, j
well, redundancy for the highest shell is 4.8, I/sigma is 3, Rmerge for
overall is 0.08 for highest shell is 0.336. I/sigma and Rmerge don't seem
quite nice...
thanks.
On Mon, Mar 17, 2008 at 11:51 AM, Partha Chakrabarti <[EMAIL PROTECTED]>
wrote:
> Hi Melody,
>
> There was a nice discussion in
Looks ok I guess.. for the highest shell, if Rmerge is less than 0.45
and I/sigma is about 2, it is worth a try.. as James said,
completeness might be from why it is incomplete.. is it something like
C2?
experts might tell us more..
Best, Partha
On Mon, Mar 17, 2008 at 11:03 AM, Melody Lin <[EMAI
Can anyone explain the rationale for treating the test set reflections
as 'unobserved' for the maps, even though they have perfectly good
observed Fo values? This doesn't make a great deal of sense to me!
Looking at the mtzdump output for the MTZ file output by Refmac, I
indeed note that for the
Gordon Research Conference on Diffraction Methods in Structural Biology
July 13-18, 2008, Bates College, Lewiston, Maine, USA
Co-Chairs: Elspeth Garman & Andrew Leslie
The 2008 Gordon Research Conference on Diffraction Methods in Structural
Biology will encompass advan
Dear all,
I am trying to install arp/warp and I am stuck with the following error:
--
Checking refmac5 installation - refmac5: Command not found.
*** ERROR ***
Cannot execute refmac5
*
Hi Phil,Thanks for your email. I did get it to work with the options you
suggested .
i.e
Toggle ON "Override automatic definition of runs to mark discontinuities in
data
Toggle ON Define Runs
Toggle OFF Use run 1 as reference run.
Setup runs as follows ( intended to exclude batches 200 to 400
Melody Lin wrote:
Hi all,
I have always been wondering... for a data set diffracting to say 2.15
Angstrom but in the highest resolution shell (2.25-2.15) the
completeness is 74%, should I use merge all the data and call it a 2.15
A dataset or I should cut the data set to say 2.25 A where the
On Mon, 2008-03-17 at 10:51 +, Partha Chakrabarti wrote:
> Not just one of them. If you are pushing it too far, you will see the
> effect in later refinement step..
And the effect in later refinement step will be the slight increase in
R-factor? IMHO, this does not justify throwing away data
I would use all the data myself and report that the model was built from a
a dataset with 74% completeness in the 2.25 to 2.15 Anngstrom shell. I
would not put the number 2.15 A in the manuscript title nor in the poster
title.
For me the acceptable completeness is 90% in the highest resolutio
Dear Mario,
it seems that inside the install script the path variable is not set and
therefore the call to refmac5 fails. We are not sure why this happend in
your case. The install script was tested with both (t)csh and bash and
something in your machine setup was not anticipated by us. Have y
All,
Below you will find the pertinent information for a job opening at the Howard
Hughes Medical Research Institute. All information can be found at this site:
http://www.hhmi.org/jobs/main?action=job&job_id=548.
If you are interested, please follow the instructions in the advertizement and
Dear all,
We would like to announce that we are organizing two courses on:
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Both will take place at the NKI at Amsterdam, at our brand new lab
space (we have not even moved y
Dear Gerrit,
Changing the alias to include the full path for refmac5 worked. Thank
you very much for your help.
I don't know if it helps you somehow, but I was running it on the same
terminal where I typed "refmac5 -i". Actually, the paths for the CCP4
programs are configured in /etc/bash.ba
Redundancy of 4.8 for a 74% complete shell (if I understand which
shell these stats are for) suggests you have assumed too much symmetry
and are rejecting a lot of reflections during scaling. Is this the
case? The I/sigma suggests you could drop the symmetry and re-scale
without losing a lo
Hi -
I would tend to argue as follows:
An I/sigI of 3, and Rmerge of 33.6% are most definitely acceptable
values with a redundancy of 4.8. Thus, despite the 74% completeness,
that data are most definitely useful and should be included in
refinement.
A good question now is why is the data
Hello all,
I apologize for the off-topic post. I have a problem with Coot being
unable to read the space group from the CRYST1 line in the PDB file.
Although the space group is specified correctly, Coot seems unable to
read it. It reads the unit cell dimensions and angles just fine - it
seems to ha
Dear all,
Thank you very much for the useful suggestions! I definitely learned a lot
from these discussions. Now looking back at my datasets, I think the
incompleteness likely results from high mosaicity (1.009) and anisotropy of
the crystal. Detector is square, but the distance is short enough fo
your CRYST1 card is most likely missing the actual space group name. You
can fix this with e.g. pdbset:
pdbset xyzin your.pdb xyzout pdb-with-spacegroup-name.pdb << eof
spac P21212
end
eof
where you replace P21212 with your actual space group name.
Tim
--
Tim Gruene
Institut fuer anorganische
Hi again,
I guess this is only a partial summary, since I still don't understand
all the issues this question raises.
Pavel Afonine reported that his extensive tests of the PDB reveals that
reproducing R values from models with TLS ADP's is a wide-spread and
serious problem. The principal pr
Thanks for all those quick replies! Im sorry my post didnt carry the
CRYST1 line.
It should have read:
CRYST1 86.316 86.316 279.245 90.00 90.00 120.00 P 65
I tried all your suggestions but I still cannot get coot to read the SG.
What is strange is that when coot starts up (coot --pdb ABC
Hi,
It may just be a typo in your letter, but there should only be
a single space between the last zero and the "P". Spacing matters
in PDB files.
Dale Tronrud
Pavan wrote:
Thanks for all those quick replies! Im sorry my post didnt carry the
CRYST1 line.
It should have read:
CRYST1 86.3
On Monday 17 March 2008 16:20, Dale Tronrud wrote:
> Hi again,
>
> I guess this is only a partial summary, since I still don't understand
> all the issues this question raises.
>
> Pavel Afonine reported that his extensive tests of the PDB reveals that
> reproducing R values from models with
2) Some files list in the ATOM "B" column the residual B after TLS
has been accounted for while others list the total B (TLS and
residual). There is no clear indication in the PDB file which
interpretation is being used.
That is a fundamental deficiency in the ex
A postdoctoral position is available to study the structure and function of
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Recent papers describing work from the lab include: Nat Struct Mol Biol. 2006
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Once again, thanks a lot for all your replies.
I just found out the problem. Ultimately it was quite a silly mistake
- I had an old and defunct SYMINFO environment variable from solve/
resolve in my .cshrc file, which clashed with the one that coot was
setting (in /sw/share/coot/setup/coot.sh). O
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