[ccp4bb] Postdoc position available in Berkeley

2019-11-01 Thread Peter Zwart
=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

[ccp4bb] Beamtime at the ALS-BCSB beamlines

2010-09-09 Thread Peter Zwart
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

[ccp4bb] Beamtime at the ALS-BCSB beamlines

2010-07-12 Thread 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 with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening

Re: [ccp4bb] Beamtime at the ALS-BCSB beamlines

2010-07-12 Thread Peter Zwart
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

Re: [ccp4bb] Wilson B and Mean B factors

2010-07-09 Thread Peter Zwart
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

Re: [ccp4bb] General user proposal deadline May 15, 2010

2010-05-12 Thread Peter Zwart
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

Re: [ccp4bb] ALS or Uni Pucks

2010-04-09 Thread Peter Zwart
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

Re: [ccp4bb] reforigin on 2FKA

2010-02-08 Thread Peter Zwart
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

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Peter Zwart
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

[ccp4bb] Beamtime at the ALS

2010-01-12 Thread Peter Zwart
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

Re: [ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread Peter Zwart
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

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

2009-12-10 Thread Peter Zwart
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

[ccp4bb] Dear friend!

2009-10-21 Thread Peter Zwart
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

Re: [ccp4bb] Software for predicting potential disulfide cross-linking sites?

2009-09-30 Thread Peter Zwart
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

Re: [ccp4bb] Summary for Anisotropic Diffraction In Refinement question

2009-09-15 Thread Peter Zwart
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 poorly

[ccp4bb] General User Proposal Deadline for PX/SAXS at the ALS: August 15, 2009

2009-08-12 Thread Peter Zwart
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

Re: [ccp4bb] Reindexing Orthorhombic

2009-04-17 Thread Peter Zwart
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

Re: [ccp4bb] Crick-Magdoff and anomalous

2009-03-23 Thread Peter Zwart
(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 contributes both to F+ and F-.  I think Peter Zwart pointed this out earlier.  There is also another sqrt(2

Re: [ccp4bb] Problems with phasing a protein (1300aa)

2009-03-20 Thread Peter Zwart
|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

Re: [ccp4bb] Problems with phasing a protein (1300aa)

2009-03-20 Thread Peter Zwart
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

[ccp4bb] Beamtime proposal deadline for ALS GU time

2009-03-12 Thread Peter Zwart
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

[ccp4bb] Deadline for ALS PX beamtime this Thursday, Jan 15.

2009-01-12 Thread Peter Zwart
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

Re: [ccp4bb] indexing choice for C2

2008-12-13 Thread Peter Zwart
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

[ccp4bb] General user proposal deadline November 15

2008-11-13 Thread Peter Zwart
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

Re: [ccp4bb] P21,C2, C2221

2008-11-07 Thread Peter Zwart
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

Re: [ccp4bb] foam dewar usage ?

2008-10-09 Thread Peter Zwart
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

Re: [ccp4bb] R32 data

2008-10-02 Thread Peter Zwart
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,

Re: [ccp4bb] truncate ignorance

2008-09-08 Thread Peter Zwart
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

[ccp4bb] PX beamtime application deadline Sept 3rd!

2008-09-02 Thread Peter Zwart
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

[ccp4bb] PX beamtime application deadline Sept 1st!

2008-08-29 Thread Peter Zwart
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

[ccp4bb] Summary: Dry shippers

2008-08-26 Thread Peter Zwart
). - Thanks a lot. Peter Zwart

[ccp4bb] ALS user meeting

2008-08-18 Thread 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

[ccp4bb] Beamtime available; Deadline for applications : May 15.

2008-05-12 Thread Peter Zwart
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

Re: [ccp4bb] space group problem

2008-05-01 Thread 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

Re: [ccp4bb] twinned?

2008-04-03 Thread Peter Zwart
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

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

2007-10-29 Thread Peter Zwart
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

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

2007-10-29 Thread Peter Zwart
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

Re: [ccp4bb] Twinning

2007-10-23 Thread Peter Zwart
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

Re: [ccp4bb] Twinning

2007-10-23 Thread Peter Zwart
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

Re: [ccp4bb] Nearly perfect twinned data????

2007-09-26 Thread Peter Zwart
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,

Re: [ccp4bb] Another twinning question

2007-09-14 Thread Peter Zwart
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

Re: [ccp4bb] small molecule refinement GUI for Mac

2007-08-31 Thread Peter Zwart
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.

Re: [ccp4bb] Strange diffraction images

2007-08-27 Thread Peter Zwart
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

Re: [ccp4bb] density histogram

2007-08-02 Thread Peter Zwart
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

Re: [ccp4bb] phenix mtz to ccp4 mtz conversion

2007-07-24 Thread Peter Zwart
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

Re: [ccp4bb] Twinning in C2 ?

2007-07-13 Thread Peter Zwart
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'

Re: [ccp4bb] DANO from PDB

2007-06-07 Thread Peter Zwart
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

Re: [ccp4bb] twin fraction varies between crystals?

2007-04-17 Thread 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

Re: [ccp4bb] phasing power ofatoms

2007-03-28 Thread Peter Zwart
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