=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
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
Sorry for the clutter: This is of course for the Aug/Sept cycle.
P
2010/7/12 Peter Zwart phzw...@lbl.gov
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
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 the
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
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 passed my
pdbset/sfall test, so I just
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 passed my pdbset/sfall test, so
I just assumed I must have done something wrong and added everything in the
CCP4 document and ITC Vol B to the list
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
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
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
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
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 j...@trimer.med.cornell.edu:
Dear All
Does anyone know a software or web-server which can predict potential
disulfide cross-linking sites?
I
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
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
|delta F|/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|/F would translate into a 10 to 12% expected
difference for individual intensities.
P
2009/3/20 Bernhard Rupp
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
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
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
use MOSFLM, XDS or D*TREK
Peter
2008/12/13, James Whittle whit...@mit.edu:
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
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
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
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
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,
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), then the above argument
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 beamtime at the ALS
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
).
-
Thanks a lot.
Peter Zwart
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 structure solution with PHENIX
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 Zwart
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
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
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
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
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 mutant
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
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, I41,
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 0.22
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 interface.
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
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
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'
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 if anything is unclear or if you have trouble running it.
HTH
Peter Zwart
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
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
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