=88480
Regards
Peter Zwart
--
P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road
Dear All,
September 15, 2010 is the deadline for the November/December 2010
Rapid Access Proposal cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are
equipped with ADSC Q315/Q315R detectors, automated sample changers and
data collection software enabling high-throughput crystal s
Sorry for the clutter: This is of course for the Aug/Sept cycle.
P
2010/7/12 Peter Zwart
> Dear All,
>
> July 15, 2010 is the deadline for the March/April 2010 Rapid
> Access Proposal cycle.
>
> All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
>
Dear All,
July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal
cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
with ADSC Q315/Q315R detectors, automated sample changers and data
collection software enabling high-throughput crystal screening a
>
>
> I've never looked at this statistics before, so I'm a bit surprised
>
So am I !
> - I was expecting a larger discrepancy between Wilson B and average B at
> low resolution. Although this is probably because PHENIX uses Peter Zwart's
> likelihood-based Wilson B estimation (Peter - what's th
Dear All,
Just a reminder that May 15, 2010 is the deadline for the July-August
2010 Rapid Access Proposal cycle for PX beamtime at the ALS. The BCSB
beamlines (5.0.1,5.0.2, 5.0.3, 8.2.1 & 8.2.2) can all be operated
remotely and are all equipped with ADSC Q315(R) detectors. Beamlines
8.2.2, 8.2.1
We have drawings available for both pucks and tools, freely available
for anybody to use:
http://bcsb.als.lbl.gov/wiki/index.php/Automounter#Technical_drawings_and_CAD_models_for_the_pucks_and_automounter_tools
At the moment, crystal positioning is the only supplier possible (they
will have the A
; > From: owner-ccp...@jiscmail.ac.uk
>> > > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
>> > > > > Sent: 27 January 2010 21:35
>> > > > > To: Francois Berenger
>> > > > > Cc: CCP4BB@jiscmail.ac.uk
>> > >
bove I
> originally found no "allowed" shifts for F432 (not sure why, but maybe
> because it was last on my list). Years later, I think it was Peter Zwart who
> pointed out to me that I was missing a few of what ought to be allowed
> origins. As I recall, at least one of them passe
Dear All,
January 15, 2010 is the deadline for the March/April 2010 Rapid Access
Proposal cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with
ADSC Q315/Q315R detectors, automated sample changers and data collection
software enabling high-throughput crystal screenin
Hi Stephen,
> R32
> H32
> R32 :H
Correct. These are all hexagonal setting. As far as I know, the
hexagonal setting of R32 (R32:H) is the first one that comes up in the
ITvA as is listed a R32. The rhombohedral/primitive setting of R32
(R32:R) comes second in the ITvA, I guess the first setting ta
> He pretends to go to the synchrotron, comes back
Thats what I do all the time. Instead, I go to lane splitters /
jupiter for pizza and beer.
P
>The way Phenix.refine refines a model with a high twin fraction is
different >(proportionality rules) which can introduce model bias, so your
model should >be pretty close to the end product. I recommend refining your
structure as >well as you can without inputting the twin law until the very
end.
Dear friend,
I want to share a wonderful thing with you.
I know a very good website: http://www.kcnshop.com/
They mainly sell new and original electronic products. Now they are
promoting their products.
The promotion will keep for 45 days.
I have bought many products from them, their products qual
I remember this question (and the answer) from 11 years ago!
http://www.ysbl.york.ac.uk/ccp4bb/1998/msg00051.html
HTH
Peter
2009/9/30 Jie Liu :
> Dear All
>
> Does anyone know a software or web-server which can predict potential
> disulfide cross-linking sites?
>
> I have solved a crystal str
> Application of a elliptical resolution boundary is justified because the
> resolution boundary from common integration programs (Denzo and Mosflm for
> example) is spherical where diffraction for anisotropic data is ellipsoidal.
> A spherical boundary would result in the inclusion of numerous poo
Dear All,
August 15, 2009 is the deadline for the October - December 2009 Rapid
Access Proposal cycle. (Please note that the ALS will be shut down
in September, 2009.)
Remote data collection is available on all beamlines at the Berkeley
Center for Structural Biology (BCSB). The NX remote
has been
extended to 17 keV, enabling the routine use of shorter wavelengths
and anomalously scattering elements such as bromine.
All beamlines of the BCSB (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2) can
all be operated remotely. Please contact Peter Zwart (sector 5
beamlines) or Corie Ralston (sector
when reindexing p212121 with -h,l,k, you get
P 21 21 21 (a+1/4,b-1/4,c-1/4)
so you should subtract 1/4 from x and add a quarter to y and z.
some tools in the cctbx are available that make this go easy
(reindexing and moving things back to a standard setting). Reruning
phaser might be the least pa
/7
> sigma(I_P)/I_P < 0.756*sqrt(N_H/MW)*fpp
>
> I_P/sigma(I_P) > 1.3*sqrt(MW/N_H)/fpp
>
> There are some obvious approximations here. Probably the biggest is
> assuming that fpp = F_H. In actual fact, anomalous differences "count
> double" since fpp contribu
> Sure, no while lines considered in the edge calc, for example.
That and (more important) that
2*abs(a-b)/(a+b) > 2*abs(sqrt(a)-sqrt(b))/(sqrt(a)+sqrt(b))
See Acta Cryst. D61, 1437–1448.
(btw, while is overrated, use for and a break statement)
p
<|delta F|>/ *c \approx < |delta I|/ I > ,
with c somewhere between 2.5 and 3.
Bijvoet amplitude ratios seem always more pessimistic then they should be.
The 4 to 5% <|delta F|>/ would translate into a 10 to 12% expected
difference for individual intensities.
P
2009/3/20 Bernhard Rupp :
> Wha
The deadline for the may/June cycle of general user time for PX in the
ALS is coming up soon (This Sunday).
The Berkeley Center for Structural Biology (BCSB) has recently
completed a number of upgrades:
Sector 8: Recent improvements include:
* A high-accuracy microdiffractometer on BL 8.2.
Dear All,
The deadline for general user proposals for PX beamtime at the ALS is
coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:
Sector 8: Recent i
use MOSFLM, XDS or D*TREK
Peter
2008/12/13, James Whittle :
> Dear all,
>
> I believe I've run across a case similar to that described recently in
> Zwart et al., Acta Cryst. (2008) D64, 99-107:
>
> "Given the pseudosymmetric nature of the lattice (pseudo-rhombohedral), C2
> can be embedded in
Dear All,
The link I send earlier was incomplete:
http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize
Excuses,
Peter
2008/11/13, Peter Zwart <[EMAIL PROTECTED]>:
> Dear All,
>
> The deadline for general user proposals for PX beamtime at the ALS is
>
Dear All,
The deadline for general user proposals for PX beamtime at the ALS is
comming up soon! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:
Sector 8: Recent improveme
Hi,
Please note that there are 3 different spacegroups directly below
C222(1), namely
C 1 2 1 41.85 181.82 119.48 90.00 90.00 90.00
C 1 2 1 181.82 41.85 119.48 90.00 90.00 90.00
P 1 21 1 41.85 119.48 93.26 90.00 102.89 90.00
[ as obtained by phenix.explore_metric_symmetry --unit_cell="41.8500
successful candidate will have the opportunity to work with
experienced software developers in the field of biophysics and
interact with users and beamline staff on SAXS beamline 7.3.3 at the
Advanced Light Source (ALS) in Berkeley California.
Interested candidates can contact me (Peter Zwart, [EMAIL
> If they really do cost $160, your best bet might be to email your friendly
> local synchrotron group and ask if they will make you something at a fraction
> of the price ...
Or just pay up. 160 USD is not a lot when compared to other
consumables likes chemicals or crystal screens. The dewars l
Hi Josiah,
The primitive cell is what is important. The primitive cells for C2
and R32:H are the same as the P1 cell you report:
(using phenix.explore_metric_symmetry)
R32:H Niggli cell: (81.728198520053866, 81.728198520053866,
81.728198520053866, 84.166443879693517, 84.166443879693517,
84.166
phenix.refine also might not (by default) use missing data in map calculation.
AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
this changed now).
When your high resolution shells are incomplete (like when using the
anisotropy server to perform elliptical data truncation, or etc
> However, when you
> need amplitudes, truncate is the way to go.
Better is to buy a detector that records amplitudes rather then intensities:
http://shelx.uni-ac.gwdg.de/SHELX/#FAQs%20smallmol
P
> I believe also that in an earlier posting Peter Zwart said he thought
> that CNS doesn't take account of the Wilson distribution when doing its
> version of the correction; if this is true (and I have no independent
> evidence that it is since I'm not a CNS user), t
Dear All,
The deadline for user proposals for PX beamtime at the ALS has been
extended to September 3, 5pm pacific time.
See my previous email for details.
Thanks
Peter
2008/8/29 Peter Zwart <[EMAIL PROTECTED]>:
> Dear All,
>
> The deadline for general user proposals for PX
Dear All,
The deadline for general user proposals for PX beamtime at the ALS is
comming up soon! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:
Sector 8: Recent improveme
shipping costs (which, as I recall, only add ~$100-200).
-----
Thanks a lot.
Peter Zwart
wars/pucks/vials and prepare them for dry-shipment and
how they and/or their shipping department checks if the dewars are
empty indeed.
Cheers
Peter Zwart
--
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biolog
nstrations are (tentative titles only) :
* Efficient screening and data collection using Mini & WebIce (Bl. 5.0.n)
Peter Zwart, John Taylor & Nick Sauter
* Data collection @ 4.2.2
Jay Nix
* SSRL & Webice
Aina Cohen
* Automated structur
ns or would like to request open beamtime,
please e-mailing [EMAIL PROTECTED]
(Please note that executed user agreements must be received by LBNL
prior to beamtime. Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)
Regards
Peter
Clemens is right of course. If you ignore the lattice centring in C2,
the cells are the same.
I was however under the impression that auto-indexing goes via the
primitive cell. Which makes the two solutions unique.
Ignoring the possible lattice translation in P2 will show up in a
Patterson functio
Take your c2 cell, go to niggli setting, double the c axis. apply
transform (-x+z,y-z,-z). now you end up with your P2 cell in the
niggli setting. you might have stromng pseudo translational symmetry
(or your unit cell is too big)
phenix.explore_metric_symmetry --unit_cell=145,44,67,90,110.5,90
Hi Bart,
important are the dimensions of the reduced cell.
in this case his uc params are 99 167 125 90 90 90. parameters of the
niggli cell are
97, 97, 125, 90.0, 90.0, 118 which is pseudo hexagonal.
[running xtriage would give this info, including an L-test and other
various tests]
HTH
P
earch Team for beamlines 5.0.1 and 5.0.2 should contact
the Head of the BCSB (Paul Adams: [EMAIL PROTECTED], 510-486-4225).
(Please note that executed user agreements and proprietary fees, if
applicable, must be received at least five working days prior to
scheduled beam time.)
--
Peter Zwart
Bea
or use phenix, which is indifferent to format and asu choice.
P
2008/2/21, Michele Lunelli <[EMAIL PROTECTED]>:
> Simon Kolstoe wrote:
>
> > I converted the resulting
> > XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac.
> >
>
>
> Sorry if this is obvious, but you shou
I am a big fan of the RvR statistic
(http://journals.iucr.org/d/issues/2006/01/00/ba5089/index.html)
This statistic is very usefull when a model is available.
When no model is present, the L test is nice as well and is relatively
robust in the presence of pseudo centring.
P
2007/10/31, Elean
> the Nz test says no twinning
and the intensity stats say this as well.
> but the Britton and H-plots give a twin fraction of
> 0.46-0.47 !
The britton and H test give an estimate of the twin fraction IF THE
DATA IS WOULD BE TWINNED. The fact it gives a non zero value does not
indicate the pres
Wilson plots are not very informative for the detection of twinning.
The spikes you see in your Wilson plots, could be due to ise ring
issues (both 3.89 and 2.24 A are at ice ring related d scapings.) The
very large mean intensity in those resolution shells could be due to
the fact that only str
Hi Dirk,
Nice cross validation flags for twin refinement do obey the twin law:
if (h,k,l) is in the free set, then (k, h, -l) should be as well.
Same is/should be true for work set btw.
In phenix, we generate test reflections that follow the lattice
symmetry (*). This means that even if you do n
try using phenix.refine and use TLS. it might help lowering Rfree (or
raising Rwork).
P
2007/10/23, john kryst <[EMAIL PROTECTED]>:
> Hi CCP4bb ,
>
> Thanks for your suggestions... here is the summary of the
> structure...
>
> I am working in deletion and point mutants. I have a
> As you see, distortion index table indicates I centered tetragonal, I
> centered orthorhombic, F centered orthorhombic, C centered monoclinic
> and triclinic as possible Bravais lattices.
>
> Data processed in I centered tetragonal gives low Rmerge in all the
> possible space groups namely I4, I
>
> RRfree Fract
> P6122 0.277 0.362
> P61 0.266 0.35
> P61 twin0.177 0.219 0.494
> P3112 0.27 0.352
> P3112 k,h,-l0.177 0.22 0.494
> P3112 -h,-k,l 0.177
What about the very nice OLEX2 gui?
http://www.dimas.dur.ac.uk/olex
Groet,
Peter
2007/8/31, William Scott <[EMAIL PROTECTED]>:
> gfortran -o platon platon.f xdrvr.c -lX11 -L/usr/X11R6/lib does the trick.
>
> export NETEXE="open"
>
> lets you use your default web browser.
>
> That's one fugly
> As a side note, Xtriage
> doesn't think things are twinned as was suggested for one some of the other
> diffraction patterns discussed earlier today.
Hi Todd,
Detection of twinning in the presence of pseudo translations / and or
NCS parallel to the twin law is difficult and using model based
te
Hi Elisabetta
Your unit cell is pseudo F222, with twin law (-h,-k,h+k+l):
iotbx.explore_metric_symmetry --unit_cell="47.7533.6191.04
90.000 103.635 90.000" --space_group=C2
(output below)
Did you rule out twinning?
Try runing phenix.xtriage for some intensity stats and/or
phenix.refine
Hi Bernard, it this is relatively easy. Copy this text:
#phil __ON__
xmanip {
input {
xray_data {
file_name = porin.mtz
labels = FOFCWT
name = map_coef
write_out =False
}
}
parameters {
action = *manipulate_miller
manipulate_miller {
task = *custom
cu
Use truncate to convert I-obs to F-obs. No format change is needed.
Peter
John Bruning wrote:
Hi,
I have an mtz file from Phenix I am trying to convert for use in
Refmac. The labels are currently:
H
K
L
I-obs
SIGI-obs
R-free-flags
I can't seem to get it to work. I am using Import, it
Hi Demetres,
not sure if this is going to be usefull, but here I go.
Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.
There is no obvious 'perfect' rel
I don't think that there is a program available to do what you want, but
What about APEX2 from Bruker?
P
Detwinning data and refining against detwinned data is not the best
thing to do, especially when you realise that detwinning data with
twin fraction larger than 45% is done using model information in CNS:
the detwinned data you get out is not experimental anymore.
Subsequently, you cannot trust yo
I suggest you go back to your images and see what is going on during indexing.
You might want to check for certain unexplained peaks to could be an
indication of reticular-non merohedral twinning: you have 30 58 118 90
90 90. If you take two unit cells and stick them on top of eachother,
you will
rself.
Since xmanip is fairly new, you will find a bug in the current release
that somehow appears when you do not read in any external xray data.
This happens however right after the mtz file in question has been
written out. This will be fixed in the forthcoming release (soonish).
Let me know
The ccp4 gui has an option that allows one to specify which executable
to run. I allways forget how to get there.
From the phenix gui there is no problem, it uses the absolute path for
executables, and (as far as I know) phaser is invoked from within
python.
Most interesting mmtbx and iotbx co
Hi Jay,
Maybe try to use the the rhombohedral setting (space group R32:R, with
unit cell 229,229,229,81,81,81 ) rather than the hexagonal one used now.
Depending on the fft algorithm used to compute structure factors for
your partial model, this can save you a chuck off memory/time.
You can
Hi Mark,
Estimating twin fractions is best done on the basis of refining it with
a model. This can be done with phenix.refine or other programs like
shelx or CNS.
The ML estimate ofd the twin fraction relies on the correctness of the
sigmas. The 0.02 is actually the lower limit the ML proced
ferences therein. The simulation tool described in this
paper is available on request.
HTH
Peter
--
Peter Zwart
Beamline Scientist,
Physical Biosciences Division
Berkeley Center for Structural Biology
Building 6, Room 2134
Tel: 510-486-4214, Fax: 510-486-5664
http://bcsb.lbl.gov
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 6R2100
Berkeley, CA 94720, USA.
--
hmmm...
is this the beginning of a potential endless loop of emails?
P
David W Borhani wrote:
Hi, David Borhani is no longer with Abbott. Please resend your email to:
[EMAIL PROTECTED]
This usually leads to a mad
chase through all possible space groups, twinning refinements, etc. and,
in my experience, often results in a lot of time being spent for no
significant improvements.
If one has a model to refine, it is actually very straightforward to
test all possible merohedral
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