Hi,
did you check in the refmac logfile that the cif file created at the
first step was actually read ?
If it is, you will have to carefully check the cif file and you ligand
structure :
1) is the ligand structure included in the PDB at the fisrt step
complete ?? Maybe you included only a part
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Dear Dipankar,
according to the log-file, the restraints-file was not read in the
second time you ran refmac5. It should otherwise be listet in the
section underneath "Information from CCP4Interface script" where it is
mentioned as "LIBOUT" instead of
Dear all,
Would anyone know of a source for recombinant enterokinase?
Best,
Elias
http://www.neb.com/nebecomm/products/productP8070.asp
Date: Mon, 12 Mar 2012 09:38:22 -0400
From: elias.fernan...@utk.edu
Subject: [ccp4bb] recombinant enterokinase
To: CCP4BB@JISCMAIL.AC.UK
Dear all,Would anyone know of a source for recombinant enterokinase? Best,Elias
Dear Elias,
Here are three sources for recombinant enterokinase:
http://www.genscript.com/protein/Z02199-Porcine_Enterokinase_Lyophilized.html
http://www.prospecbio.com/Enterokinase/?gclid=CMuXvK6-4a4CFUQUKgodjGwlXQ
http://www.neb.com/nebecomm/products/productP8070.asp
Hope it helps!
Take Care,
Hi All, I misspoke - what I'm looking for is a source for an expression
system for recombinant enterokinase.
Elias
Subject: recombinant enterokinase
Dear all,
Would anyone know of a source for recombinant enterokinase?
Best,
Elias
Hi -
I agree with Garib that its likely a pseudo-translation issue.
I also agree with that the advice he gives is correct, but ...
... since I am evidently less smart to follow all these steps,
I like to use phenix.xtriage that will tell me if there is pseudo-
translation or not,
and will give
Hi all,
I have a homotetrameric coiled-coil domain sample with 45aa per each.
While I store this sample at 4oC, the sample looks clear w/o any
particles. But when I took out the sample to my bench at r.t, I can see
there are precipitates (as stack of needle like particles) at the bottom
of
Which kind of buffer you use? If it is Tris, then temperature change
will cause pH change.
Actually, this is a good way for crystallization.
Kevin
On Mon, Mar 12, 2012 at 9:02 AM, Min-Kyu Cho wrote:
> Hi all,
>
> I have a homotetrameric coiled-coil domain sample with 45aa per each. While
> I st
Yes, the current version of Phaser will do the same test that xtriage carries
out, and if it finds a sufficiently high non-origin Patterson peak, it will
automatically characterise the translational NCS and use this for molecular
replacement. This is working pretty well in our tests.
In the ne
Airlie points out that what I said about the ccp4i interface wasn't correct!
In order to keep the ccp4i interface in synch with the version of Phaser, we've
started distributing the ccp4i files with the source code. The ones on our
website are for an older version of Phaser, but the latest one
Dear CCP4bbers,
>
> Is there any tool to calculate the Matthews coefficient from a
> crystallographic model of RNA-protein complex?
>
> Thanking you.
> James.
>
Just want to point this out although it's pretty easy to remove these
hydrogens manually...
Or, maybe this only happened to me.
Xun
--
Department of Molecular and Structural Biochemistry
North Carolina State University
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Dear James,
I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base
to calculate the solvent content by hand.
Regards,
Tim
On 03/12/2012 06:35 PM, james09 pruza wrote:
> Dear CCP4bbers,
>>
>> Is there any tool to calculate the Matthew
matthews_coef ?
-- Ian
On 12 March 2012 17:35, james09 pruza wrote:
>
>
>
>> Dear CCP4bbers,
>>
>> Is there any tool to calculate the Matthews coefficient from a
>> crystallographic model of RNA-protein complex?
>>
>> Thanking you.
>> James.
>
>
I am using KPi buffer at pH 5.5, 100mM KCl, 2mM beta-mercaptoethanol, 0.02%
NaN3.
Yes, I agree I should check CD melting curve to see temperature preference
of my protein.
Min-Kyu
| -Original Message-
| From: Kevin Jin [mailto:kevin...@gmail.com]
| Sent: Monday, March 12, 2012 11:16 A
... or rwcontents ?
-- Ian
On 12 March 2012 17:35, james09 pruza wrote:
>
>
>
>> Dear CCP4bbers,
>>
>> Is there any tool to calculate the Matthews coefficient from a
>> crystallographic model of RNA-protein complex?
>>
>> Thanking you.
>> James.
>
>
Has anyone successfully processed images from the new Pilatus detector?
I can visualize them and auto index but not refine the cell or integrate!
Oh I'm using version 7.0.7
Cheers
Dean
SSRL 12-2 uses a Pilatus 6M and can be processed in Mosflm or XDS without
problems (have not tried HKL or D*Trek).
Do you have the right beam center ?
Jürgen
On Mar 12, 2012, at 2:22 PM, Dean Derbyshire wrote:
Has anyone successfully processed images from the new Pilatus detector?
I can visualiz
James,
For a detailed analysis of Matthews coefficients (Matthews probabilities), you
can use this web-based tool:
http://www.ruppweb.org/Mattprob/
There is a pull-down menu to select the sample type, and one choice is
"protein-DNA complex." Perhaps someone can correct me if I'm wrong, but I c
Hi Dean
I'd get in touch with the Mosflm authors and ask them for help ;-)
A copy of the mosflm.lp file (or the date-stamped version from
iMosflm) would be useful in diagnosing the problem.
On 12 Mar 2012, at 18:22, Dean Derbyshire wrote:
Has anyone successfully processed images from the ne
Min-Kyu,
This sounds like to be a hydrophobicity ~ temperature issue (as Kevin pointed
out, pH gets involved too).
If your protein is sensitive in this regards, it could form different
oligomerization states at diff temp, associated
with diff solubility. You may want to crystallize it at diff
> I can't imagine the results would be very different for protein-DNA vs.
> protein-RNA.
The reason protein-nucleic acids is an extra category in mattprob is largely
due to poorer statistics
resulting from limited sample size and hence no reliable resolution dependence
can be computed.
In add
Hi again, it's the 2M detector I'm having problems with. Got different data
from a 6M and yep that works a dream.
?
:0)
From: Harry [ha...@mrc-lmb.cam.ac.uk]
Sent: 12 March 2012 20:30
To: Dean Derbyshire
Cc: Harry; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb]
Is there a difference in the psv between DNA and RNA? I assumed (possibly
incorrectly) that they would be very close if not exactly the same? Is mattprob
more applicable to protein-DNA complexes than Protein-RNA complexes?
Thanks for the insight,
Mike
- Original Message -
From: "Bern
Hi CCP4bb,
I would like to ask about "envelope phasing" - specifically with SAXS data.
There are papers (1) and tutorials (2) describing how this might be
done, but I have also found comments on the ccp4bb, such as this one
(http://www.proteincrystallography.org/ccp4bb/message11690.html) which
ar
Could be one of those weird behaviors displayed by detergents where cloud
point anomalously changes with temperature...
Artem
On Mar 12, 2012 1:11 PM, "Min-Kyu Cho" wrote:
> I am using KPi buffer at pH 5.5, 100mM KCl, 2mM beta-mercaptoethanol, 0.02%
> NaN3.
>
> Yes, I agree I should check CD mel
Hi David -
I think you have four hurdles to overcome:
1. How good is a SAXS envelope
2. How will you place it in the right place
3. How will you extend from ~15-20 A to around 4 A
4. How will you extend from 4 A to beyond
Steps 2 and 4 might be the easiest - albeit far from trivial.
Point 1 can
I remember I saw the similar problem caused by beta-mercaptoethanol.
Kevin
On Mon, Mar 12, 2012 at 1:29 PM, Artem Evdokimov
wrote:
> Could be one of those weird behaviors displayed by detergents where cloud
> point anomalously changes with temperature...
>
> Artem
>
> On Mar 12, 2012 1:11 PM,
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The number 380A^3/base I gave results from a decent number of nucleic
acids-only PDB files I once analysed with the 'volume' program from
ccp4. I cannot think of an application where knowing the solvent content
must be known to more than 1%, so I bet t
Point 3:
Use the saxs model for preliminary phasing of your HA derivative
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD
My memory is not as good as it used to be, but I think that I indeed got
the number of 140 cubic Angstroms per amino-acid from Kevin. It has
worked fine ever since, and is how hkl2map calculates the solvent
content for proteins.
George
On 12.03.2012 21:40, Tim Gruene wrote:
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Hi Francis,
As you may have guessed - my question is stems from my recent
acquisition of some native data for a protein that I have lots of SAXS
data for.
I suspect that more conventional MR is unlikely to work in this case
as I only have a half-decent phasing model for ~30% of the protein (2
cop
Hi Kevin,
Could you tell me more detail about beta-mercaptoethanol problem?
Min-Kyu
| -Original Message-
| From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
| Kevin Jin
| Sent: Monday, March 12, 2012 3:32 PM
| To: CCP4BB@JISCMAIL.AC.UK
| Subject: Re: [ccp4bb] My
Dear David,
I would remind that the "molecular-replacement positionning" of molecular
envelopes and some methodological features (in comparison with a conventional
MR) of this have been discussed in :
Urzhumtsev & Podjarny (1995). "On the Solution of the Molecular Replacement
Problem at Very
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