Dear all,
Thank you very much for your suggestions.
I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data
would be enough for PDB.
Best wishes,
Vinson
发件人： Pavel Afonine
收件人： PHENIX user mailing list
抄 送： Vinson LIANG
发送日期： 2010/10/22 (周五) 12:44:58 上
Hi Jerry,
Try parameters that slow the rate of protein production, such as
expressing at lower temperature, using less IPTG/inducing agent, or
using a weaker promoter.
Good luck,
Ho
It's more complicated than that, since the tricky thing is to distinguish
between reflections related eg by a putative crystallographic two-fold and by a
parallel non-crystallographic two-fold, which would give very similar intensity
relationships. Pointless does try to score these alternative m
Have you thought about a quick dip in Paratone N or other oils then
immediately plunging into liquid nitrogen? I would make a 65% Paratone
N/35% Dioxane mix, then run the crystal thru it and snap freeze in
liquid nitrogen.
Good luck!
Bryan
From: CCP4 bulletin board [mailto:ccp...@jiscmail.
On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:
>
> "if the data really looks like P21--" what are the criteria for that?
This is a straightforward statistical question.
In testing for a possible 2-fold, you want to know:
Do two random reflections related by the putative 2-fold a
Having grown crystals with dioxane as precipitant, I can tell you that
harvesting them isn't easy - as is the case for most crystals grown in volatile
precipitants. At the time, we used an increased amount of dioxane plus
2-propanol as additive to further stabilize the crystal. (Yes, that make
Well no, I never did during my crystallography training: it seems to
be a change of definition that's occurred fairly recently, without
recognition of the fact that the original definition is still in use,
particularly in mineralogy of course, where, unlike often is the case
with protein crystals,
Hi Clemens,
Sorry to be picky and start the 'definition game' over again, but
'Miller indices' are strictly not the numbers that index X-ray
reflections that everyone is familiar with (whether observed or not!).
Miller indices were introduced in 1839 by the British mineralogist
William Hallowes M
Thank you very much. I am in total agreement with you that HL coefficients are
better description of the phase probability and in fact I have been using the
HL coeffs all these times for phase combination and density modification. My
earlier post was just to make it easy for a comparison betwee
But we're still talking about crystals, right? The whole reason for
trying to crystallise our proteins/DNA/RNA is because we ideally want
a perfect arrangement of molecules. So taking as a starting hypotheses
the conservative approach that if the data really looks like P21 it
probably is P21 seems
Hi Ed,
On Thu, Oct 21, 2010 at 02:19:34PM -0400, Ed Pozharski wrote:
> > * how the refinement in the lower-symmetry spacegroup is done - since
> >there is a real danger (in case it is the high-symmetry spacegroup
> >after all) that because of model bias and poorer (independent
> >obse
Hi,
> I think that when you say "as if they were independent," you are begging
> the question. You could say that refining in higher symmetry treats the
> molecules "as if they were the same." Further, it really assumes more to
> posit that they are the same.
But we're still talking about cr
On Thu, 2010-10-21 at 18:59 +0100, Clemens Vonrhein wrote:
> I think I understand what you're getting at: you have a lower symmetry
> with a NCS axis that is basically perfectly aligned with the
> corresponding crystallographic axis in the higher symmetry
> spacegroup. And the only part of the mode
On Thu, 2010-10-21 at 12:58 -0500, Jacob Keller wrote:
> On the other hand, if somehow a few sidechains became systematically
> different between molecules in the p1 cell, it *would* make sense to
> refine
> in p1
And sometimes (but rarely) such differences become detectable at high
resolution (
Hi Ed,
On Thu, Oct 21, 2010 at 12:18:31PM -0400, Ed Pozharski wrote:
> Let's say I have a ligand on symmetry axes and so it appears in two
> conformations. If I reduce symmetry, there are two possible scenarios.
>
> a. In lower symmetry, ligand still appears in two conformations. Shall
> use hi
The "black eye" comes not from the treatment of the observations, but from
the
treatment of the model. If you want to refine the same model against
lower
symmetry and/or unmerged data - go right ahead. I think the result will
not
usually be an improvement, but in some cases this may work aroun
It should be straightforward to work out what you need to do to the
Phenix output to make it acceptable to TLSANL. All I need is the
piece of Phenix documentation that defines the TLS tensors that you
are using.
Cheers
-- Ian
On Thu, Oct 21, 2010 at 3:55 PM, Bryan Lepore wrote:
>> documentatio
And if you are not so into reading papers, you can use this database
http://idb.exst.jaxa.jp/db_data/protein/search-e.php?
Jürgen
P.S. Who wants to write an App for that, wouldn't this be very handy at the
beamline ? I take 5% of the income for the idea :-)
-
Jürgen Bosch
Johns Hopkins Bloomberg
Not to forget
J. Appl. Cryst. (1996). 29, 584-587[ doi:10.1107/S0021889896004190 ]
Glycerol concentrations required for cryoprotection of 50 typical protein
crystallization solutions
E. F. Garman and E. P. Mitchell
Which prompted the McFerrin and Snell work.
Also worth checking out (and I a
On Thu, Oct 21, 2010 at 11:42 AM, Ian Tickle wrote:
> There are a number of things that don't look right here, both with the
> Refmac and the Phenix runs: [...]
interesting, thanks for these comments.
> S should not have been symmetrized
to actually display the principal axes in molscript, i me
Because refining in the (right) higher symmetry space group leads to a
better model.
On Thu, 2010-10-21 at 11:34 -0500, Jacob Keller wrote:
>
> I have heard many times that it is a black eye to refine in a
> lower-symmetry spacegroup, but I could never really understand why.
> The higher symmetr
On Thursday, October 21, 2010 09:34:58 am Jacob Keller wrote:
>
> I have heard many times that it is a black eye to refine in a lower-symmetry
> spacegroup, but I could never really understand why. The higher symmetry
> could be considered merely a helpful theoretical lens to improve
> signal-t
How you choose to make use of (or ignore) crystallographic symmetry comes down to your
view of what constitutes the "best" model for the sample you're studying. How
similar do you believe the molecules are in your crystal? If you describe the model in a
higher symmetry space group, you believ
I have heard many times that it is a black eye to refine in a lower-symmetry
spacegroup, but I could never really understand why. The higher symmetry could
be considered merely a helpful theoretical lens to improve signal-to-noise, and
therefore imposing higher symmetry on the data could be see
Clemens,
I don't think anyone suggests to use unmerged data and such. I think
there is important difference in what Mohinder describes.
Let's say I have a ligand on symmetry axes and so it appears in two
conformations. If I reduce symmetry, there are two possible scenarios.
a. In lower symmetr
Hi Jerry,
A great reference for initial cryocondition searches for many "standard"
crystallization solutions is the tables in:
J. Appl. Cryst. (2002). 35, 538-545 [ doi:10.1107/S0021889802009238 ]
The development and application of a method to quantify the quality of
cryoprotectant solutions
You pick the Rfree flags in the high-symmetry space group, and then use
"CAD" with "OUTLIM SPACE P1" to symmetry-expand them to P1 (or whatever
you like).
Things get trickier, however, when your NCS is close to, (bot not
exactly) crystallographic (NECS?). Or if you are simply not sure. The
Hi Herman,
On Thu, Oct 21, 2010 at 05:31:51PM +0200, herman.schreu...@sanofi-aventis.com
wrote:
> If you process your data in a lower symmetry space group, you will have
> more unique reflections, since reflections which are related by the
> higher symmetry will be avaraged during scaling in a hi
Dear all,
How would one properly select reflections for R-free in these situations?
Presumably if the selection is done in P1 then it mimics twinning or high NCS,
such that reflections in both the work and free set will be (potentially?)
related by symmetry.
-Christina
_
There are a number of things that don't look right here, both with the
Refmac and the Phenix runs:
1. The Refmac T22 looks too small compared with T11 & T33, unless it
really is highly anisotropic, but this would be unusual!
Alternatively the elements of T (& possibly L) somehow got in the
wro
Dear Mohinder,
On Thu, Oct 21, 2010 at 01:05:42PM +0100, Mohinder Pal wrote:
> The question is , is it a good practice to solve this structure in
> P1 and P21 even if the data has higher symmetry?
On a slightly philosophical note regarding the final model (and not
necessarily the 'good practice'
Dear Mohinder and Ed,
If you process your data in a lower symmetry space group, you will have
more unique reflections, since reflections which are related by the
higher symmetry will be avaraged during scaling in a higher symmetry
space group (i.e. a 2fold or 3fold axis), while in lower symmetry s
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes. You can th
> documentation
then i conclude the TLS protocol in refmac is markedly different from
phenix (i know this is not strictly a ccp4 question). cf. :
refmac:
TLS
RANGE 'A 245.' 'A 252.' ALL
ORIGIN14.019 -10.476 -35.068
T 0.4974 0.0372 0.3453 0.0674 0.2984 0.0431
L 21.5463
Hi Bryan
That would obviously depend on the precise definition and order of the
T, L & S tensor values that phenix writes out; not being a phenix user
I can't help you there, but I assume that the phenix documentation
will tell you all you need to know. The format required by TLSANL is
defined in
[ ccp4 6.1.3 ]
i have some phenix TLS tensors i'd like to evaluate in tlsanl [*].
are there specific conversions/transformations to be wary of when
setting up the job or interpreting the output?
-bryan
[*] originally posted on phenix BB with some gory details.
Hi
Since you're using iMosflm to process the data, it is well worthwhile running
the "Quickscale" task following integration (I would actually run it after
integrating ~5 - 10 degrees of data) to see if the true crystal symmetry
determined by analysing agreement of the intensities of symmetry r
Dear Mohinder,
What one should really do is to provide an accurate model (including the
space group) of what is taking place in the crystal. For example, there
was this case reported by Morales et al. (2000, Acta Cryst sect. D56,
1408-1412) of a complex of 2 proteins (i.e. identical situation
Dear CCP4BB members,
I have solved a protein-drug complex structure in P21212 space group. In this
structure, the drug molecule is falling on the two-fold symmetry axis having
averaged electron density with 0.5 occupancy. We tried a lot to crystallize
this protein-drug complex in different s
Hi George,
On Wed, Oct 20, 2010 at 04:58:34PM -0700, Goragot Wisedchaisri wrote:
> Hi,
>
> I have helices that I did rigid body refinement with Phaser (after
> phased rotation and phased translation in Molrep). I compare FOM
> output by Phaser to the FOM computed by sigmaA using the Phaser
> refi
Dear All,
At last, registration and details of the BSG Winter Meeting can be found
at:
http://www.reading.ac.uk/biologicalsciences/businessdevelopment/biosci-B
CAwintermeet.aspx
We look forward to welcoming you to Reading!
Yours,
Kim Watson
Being lazy I would just do refinement with REFMAC and let it generate
the SigmaA values.. then try rebuilding with either buccaneer or
Arp/Warp.They willboth generate weighting terms based on the Rfactors.
Eleanor
On 10/21/2010 12:58 AM, Goragot Wisedchaisri wrote:
Hi,
I have helices that I
I think REFMAC will generate anappropriate SSBOND entry in the pdb for
you if you run it from the GUI with Review restraintsoption
Eleanor
On 10/20/2010 08:40 PM, Seema Mittal wrote:
Hi All,
I have engineered intra-molecular disulfide bond in my protein monomer.
The protein functions as a homo
Dear Vinson, Liang
have a look at the penultimate table from
mtzdmp your_mtz_file.mtz
where your_mtz_file.mtz is the mtz-file you are using to deposit/ for
refinement.
That second last table lists the columns which are present in your mtz-file,
their types and names and should give a clue what
Jerry McCully,
35% dioxane should be sufficient depending on the other components in your
buffer.
Yet, it is always advisable to try a few alternatives:
Try an extra 5-10% glycerol or ethylene glycol.
This might reduce the increase in mosaicity due to cooling shock.
If what you are cr
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