[ccp4bb] opening in Zbyszek Otwinowski lab

Google Scholar profile and other information about you that you consider to be the most important. Although the deadline for the application is February 15th, I will be interviewing candidates by Skype or in person (for Texas-based applicants) as soon as they are identified. Zbyszek Otwinowski UT

Re: [ccp4bb] ligand binding and crystal form

again. Zbyszek Otwinowski > Dear Veronica, > > with 1st, 2nd, 3rd map you mean the density for the same dataset after > three consecutive cycles of building-refining or three different maps from > three different crystals? > If it's the first case, it could be fine, it may

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

be achieved in SUPCOMB. regards Ashok Nayak CSIR-CDRI, Lucknow India Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353

Re: [ccp4bb] Data reduction

, Scalepack output says 98.8% complete data but after converted to .mtz file it reduced to 64%. I have tried in CCP4 and phenix both. How is it possible? Ayan Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353

Re: [ccp4bb] Space group numbers

as far as XDS is concerned: it just needs to know that the space group is P222. I can even tolerate C2 from XDS since where necessary it will get auto-re-indexed to I2 on first entry into the database (but never subsequently!). Cheers -- Ian Zbyszek Otwinowski UT Southwestern Medical Center

Re: [ccp4bb] correlated alternate confs - validation?

for other packing contacts; however, for conformations close to rotational axis, symmetry operator cannot preserve conformer ID, and this issue cannot be avoided. Zbyszek Otwinowski I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell

Re: [ccp4bb] definitions of unique reflections

both types of completeness in the publication and in the deposit, even if there is no such custom yet. Zbyszek Otwinowski There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. Unique Reflections My definition is all the possible

Re: [ccp4bb] Help in Cell content analysis

scattering. An alternative explanation is that you crystallised a proteolitic fragment of your protein. Zbyszek Otwinowski Dear all i have a small query to ask and seek your suggestions: I have collected a data for a protein with 324 residues and processed at its best in P212121. So Matthews

Re: [ccp4bb] Reprocess data with new resolution cutoff?

to lower resolution will change anything other than overall R-merge and other R-statistics. To calculate these statistics it is enough to re-merge the data with lower resolution. Zbyszek Otwinowski Hi all, This is a basic question and I'm sure the answer is widely known, but I'm having trouble

Re: [ccp4bb] metals disapear

does not matter! It is an urban legend that shorter wavelength will help. I remember it being debunked two decades ago, and somehow it is still alive. Zbyszek Otwinowski -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Dean, this is probably a very common observation: X-rays produce

Re: [ccp4bb] small molecule crystallography

= A46BEE1A -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582 Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX

[ccp4bb] Error in ccp4lib?

for reflections with initial h not equal to zero, but gives wrong result for 0 k l reflections. Zbyszek Otwinowski Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu

Re: [ccp4bb] Error in ccp4lib?

hklout newfile.mtz labi file 1 allin end I think (and hope) that the data and phases will be converted correctly to the CCP4 asymmetric unit. Eleanor On 25 Mar 2014, at 09:16, Zbyszek Otwinowski wrote: I am reading an external file, which contains phases and ABCDs in the space group P43212

Re: [ccp4bb] twinning problem ?

and can change quite a lot. Cryo-cooled crystals definitely can have high degree of internal non-isomorphism resulting from this effect. Zbyszek -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys

Re: [ccp4bb] twinning problem ?

crystals. However, this requires separate data set collection rather than mixing such crystals during one rotation sweep. Presence of multiple, similar unit cells in the sample is completely different and unrelated condition to statistical disorder. Zbyszek Otwinowski Not sure I understand why

Re: [ccp4bb] twinning problem ?

. Zbyszek Presence of multiple, similar unit cells in the sample is completely different and unrelated condition to statistical disorder. Agreed! Jacob -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353

Re: [ccp4bb] twinning problem ?

[PubMed - indexed for MEDLINE] -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu

Re: [ccp4bb] twinning problem ?

. Zbyszek Otwinowski Hi, If there's an NCS translation, recent versions of Phaser can account for it and give moment tests that can detect twinning even in the presence of tNCS. But I agree with Eleanor that the L test is generally a good choice in these cases. However, the fact that you see

Re: [ccp4bb] Data processing - twinned xtals

twinning issues during crystal growth Thanks in advance ! Mahesh[image: Inline image 2][image: Inline image 3] Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353

Re: [ccp4bb] Data processing - twinned xtals

twinning issues during crystal growth Thanks in advance ! Mahesh[image: Inline image 2][image: Inline image 3] Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Zbyszek Otwinowski UT Southwestern Medical

Re: [ccp4bb] Data processing - twinned xtals

that the particular crystal presented is twinned or highly mosaic, so chances are good that this project will be solved. Zbyszek Otwinowski Hi CCP4 folks I have a data set which is looks twinned ( see the image-1 - I zoomed on to the image so that one can spot the twinning. Furthermore

Re: [ccp4bb] rmerge

Dear All, The purpose of statistics in the output of Scalepack is to help the experimenter to assess the data. The question is, what is the purpose of R-merge statistics and its usefulness when its value exceeds 100%? When Scalepack was originally written 20 years ago, I made a decision to

Re: [ccp4bb] Strange density in solvent channel and high Rfree

in a lower symmetry. Zbyszek Otwinowski Dear all, We have solved the problem. Data processing in P1 looks better (six molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules in ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round of refinement (without put waters

Re: [ccp4bb] refining against weak data and Table I stats

The difference between one and the correlation coefficient is a square function of differences between the datapoints. So rather large 6% relative error with 8-fold data multiplicity (redundancy) can lead to CC1/2 values about 99.9%. It is just the nature of correlation coefficients. Zbyszek

Re: [ccp4bb] P4132 vs. F23

Space groups F23 and P4132 are not subgroups of each other (without invoking pseudotranslational symmetry) so they cannot be related by twinning. The end of theoretical analysis. Zbyszek Otwinowski You need to say what the cell dimensions are for these 2 options.. Eleanor On 29 May 2012

Re: [ccp4bb] How to evaluate Fourier transform ripples

. Consequently, the answer is that typically one should not see ripples. Ripples should not be confused with the effect of electron density maps being smoothed by vibrations and other forms of disorder. Zbyszek Otwinowski Dear All, Hi. I was asked in a manuscript revision to discuss about

Re: [ccp4bb] Y-Chi2 running out of chart

cooling rates and variability in the crystal lattice. Merging statistics should be acceptable, however they may not be perfect. Better cryo-cooling is likely to help. Zbyszek Otwinowski Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts

Re: [ccp4bb] Change cell parameter

will change the beta angle automatically. Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Zbyszek Otwinowski UT

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

restraints on U (square root of B) rather than on Bs themselves. It is not we who cram too many meanings on the B-factor, it is the quite fundamental limitation of crystallographic refinement. Zbyszek Otwinowski The fundamental problem remains: we're cramming too many meanings into one number [B

[ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

thread, representing poorly-ordered (so called 'disordered') side chains by the most likely conformer with appropriately high B-factors is fully justifiable, and currently is probably the best solution to a difficult problem. Zbyszek Otwinowski - they all know what B is and how to look

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

a model-building like approach. The test of the success of such approach would be a substantial decrease of R-free values. If anybody can show it, it would be great. Zbyszek Dale Tronrud On 3/31/2011 9:06 AM, Zbyszek Otwinowski wrote: The B-factor in crystallography represents

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

. Zbyszek Frank von Delft wrote: This is a lovely summary, and we should make our students read it. - But I'm afraid I do not see how it supports the closing statement in the last paragraph... phx. On 31/03/2011 17:06, Zbyszek Otwinowski wrote: The B-factor in crystallography represents

Re: [ccp4bb] data processing deviations chisq

. Hope that helps, Zbyszek Otwinowski Hi all, I have collected one iodine soaked data in our home source, and processing the data using HKL2000. Exposure time per frame is 5min/1 degree. While processing I have noticed that the Chisq values, cell parameters and rotation change Vs frame

Re: [ccp4bb] Merging data to increase multiplicity

the differences between programs). But that brings me to my last point - a wiki article does not count as a paper. best, Kay Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353

Re: [ccp4bb] Problem with finding of spots

to eliminate peaks at higher resolution during autoindexing and then extend the resolution during the refinement. Sometimes it helps for very mosaic crystals. Zbyszek Otwinowski Dear colleagues, I am working on one dataset that is hard to process. The data are about 3A of resolution. As we

Re: [ccp4bb] What makes the difference between 2 composite omit maps?

about which one is more appropriate for the sigmaa-weighted 2mFo-DFc composite omit map. (mFo is what I generated from the SIGMAA output) Thanks for any suggestions! Best Regards, Hailiang Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816

Re: [ccp4bb] What makes the difference between 2 composite omit maps?

Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353

Re: [ccp4bb] Calculating R-merge between 2 mtz files.

files (which are very similar) and calculate the R-merge between them. I tried looking into CCP4 and Phenix, but could not find a direct path. Does anybody know how I can do this R-merge calculation? Best regards, Jason Porta -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry

Re: [ccp4bb] data reduction

in Scalepack as such. Zbyszek Otwinowski Can you send a bit of your scalepack unmerged data - that would allow us to check format and pointless behavior.. It sounds a bit like a scalepack problem though.. Eleanor Alexandra Deaconescu wrote: Dear all: I am trying to solve a structure from

Re: [ccp4bb] Mosaicity beam divergence

is used), denzo overestimates it somewhat. -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu

Re: [ccp4bb] Scalepack error model?

by user, they can be refined iteratively by experimenter by adjusting parameters in subsequent runs of scalepack, but most of the time it is not required. New version will adjust all these parameters automatically. Zbyszek Otwinowski Richard Gillilan wrote: Thanks Joe and others. Bits