[ccp4bb] Positions available at the High Energy Accelerator Research Organization (KEK) - Japan
Dear all -- for those interested, we have few good positions opening at our institute. You don't want to miss the chance to come and work in this wonderful country that is Japan!!! Please have a look at the links below: http://www.kek.jp/intra-e/jobs/ Kind regards. -- Leo -- --- Chavas Leonard M.G., Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Accelerator Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan --- Phone : +81(0)29-864-5642 (4901) Fax : +81(0)29-864-2801 E-mail : leonard.cha...@kek.jp --- Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo ---
Re: [ccp4bb] peculiar twinning case
Dear Ed, You might well have a case of something called "lattice-translocation disorder", which is indeed an intermediate type of disorder with partially coherent interference between crystal domains related by non-lattice translations. Take a look at a recent paper on the subject (for instance, Acta Cryst. D65, 980-988) and at the references in it. This type of disorder has a long and distinguished history in protein crystallography, starting with a paper by Bragg & Howells in 1954 (Acta Cryst. 7, 409-411). Good luck! Gerard. -- On Fri, Oct 15, 2010 at 06:08:09PM -0400, Ed Pozharski wrote: > A couple of twinning-related questions. > > I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA > itself is not palindromic and has sticky ends located asymmetrically > with respect to the protein (dimer). > > DNA contains a single fluoro-uracil which is flipped into the active > site. This 3A structure can be easily refined down to Rf~35%, at which > point difference density tracing the fluoroU and adjacent basepairs of a > "self-superimposed" dimer is visible in the active site of the second > monomer. > > The dimer two-fold axis are aligned with the bisector of the (a,b). > Thus my first question - do I understand correctly that this corresponds > exactly to (k,h,-l) operator which is one of the possible twinning > operators in P65? > > When I try twin refinement in Refmac, the Rfree drops some 3% and > reported twinning fraction is 10%. It's great to have the lower Rfree, > of course, but I doubt that 10% occupancy would give me a detectable > density (I see mainly phosphate, but the fluoro-U moiety is rather clear > too). And indeed, the difference density remains after accounting for > twinning. > > So I tried the "dual model", where I have two copies of the whole > assembly, with the second one obtained by rotation around dimer axis. > The Rfree drops another 3%, and the difference density is now accounted > for, but the occupancy optimized for the lowest Rfree is about 50%. > > Thus my second question - since twinning appears to be related to the > same spatial transformation, why it doesn't account for it? And in more > general sense - what is going on in this lattice? > > Afaiu, the twinning and dual model contribute to the Fc in different > ways. For twinning part, the Fc=sqrt(|F1|^2+|F2|^2), whereas for dual > model Fc=F1+F2 with phases included. Now, does this mean that I somehow > have two types of twinning in this crystal - "coherent" (at 50%) and > incoherent (at 10%)? Or is it that both description are correlated - in > which case I don't understand why I get an additional drop when the two > are combined. > > It may also be important that two-fold dimer axis are not exactly (but > close) at the bisector - the polar angles reported by superpose are > (87.91,-116.242,179.987). > > I'll appreciate any suggestions, > > Ed. > > -- > Edwin Pozharski, PhD, Assistant Professor > University of Maryland, Baltimore > -- > When the Way is forgotten duty and justice appear; > Then knowledge and wisdom are born along with hypocrisy. > When harmonious relationships dissolve then respect and devotion arise; > When a nation falls to chaos then loyalty and patriotism are born. > -- / Lao Tse / -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Reindexing scaled data
On Sunday, October 17, 2010, Daniel Bonsor wrote: > Hi all, > > This maybe a simple/stupid question. I collected data at the synchrotron, > integrated and scaled the data in P222 using HKL2000, though I should of > scaled the data as P212121. Stop right there. You were correct to index and integrate in P222. This is the point group. The integration is valid for all space groups within the point group. If you later on decide that the space group is P212121, no re-indexing is necessary. Certainly no re-scaling is necessary. A slight problem can arise with some programs if the space group turns out to be P21212 or one of the other members of the point group where not all of the axes exhibit a 2_1 screw. In this case the canonical ordering of the axes may change. But even so you would not need to rescale the data, only permute the indices. Ethan > > When I try to reindex using Reindex I get a message of > > You are changing the symmetry of merged data are you SURE you know what > you are doing > WARNING: ** Symmetry change of merged data ** > > I am unsure of what I am doing in this case. Currently I cannot reprocess the > data as I do not have a working version of HKL2000. So my question is can I > reindex scaled data and what I should be doing with the GUI of reindex? > > Thanks in advance for advice. > > Just in case it is important my cell dimensions are 109.9280 160.3030 > 186.2200 90. 90. 90. and the resolution is 2.7 Angstrom.
Re: [ccp4bb] Reindexing scaled data
Try pointless first with your P222 data and as output option it will provide you the most likely space group. The warning in the GUI is just a warning, maybe P21 21 21 is not the right space group that's why you get the warning :-) In terms of reprocessing your data, you are not dependent on HKL2000, take Mosflm or XDS no license required, hassle free reprocessing of your data. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Oct 17, 2010, at 3:34 PM, Daniel Bonsor wrote: > Hi all, > > This maybe a simple/stupid question. I collected data at the synchrotron, > integrated and scaled the data in P222 using HKL2000, though I should of > scaled the data as P212121. > > When I try to reindex using Reindex I get a message of > > You are changing the symmetry of merged data are you SURE you know what > you are doing > WARNING: ** Symmetry change of merged data ** > > I am unsure of what I am doing in this case. Currently I cannot reprocess the > data as I do not have a working version of HKL2000. So my question is can I > reindex scaled data and what I should be doing with the GUI of reindex? > > Thanks in advance for advice. > > Just in case it is important my cell dimensions are 109.9280 160.3030 > 186.2200 90. 90. 90. and the resolution is 2.7 Angstrom.
[ccp4bb] Reindexing scaled data
Hi all, This maybe a simple/stupid question. I collected data at the synchrotron, integrated and scaled the data in P222 using HKL2000, though I should of scaled the data as P212121. When I try to reindex using Reindex I get a message of You are changing the symmetry of merged data are you SURE you know what you are doing WARNING: ** Symmetry change of merged data ** I am unsure of what I am doing in this case. Currently I cannot reprocess the data as I do not have a working version of HKL2000. So my question is can I reindex scaled data and what I should be doing with the GUI of reindex? Thanks in advance for advice. Just in case it is important my cell dimensions are 109.9280 160.3030 186.2200 90. 90. 90. and the resolution is 2.7 Angstrom.
[ccp4bb] Big difference between anomalous map and density modification map
Dear All, I have a MAD dataset at 4Å and shelxD can find clear-cut 10 solutions (my protein has 12 methionines). I ran autosharp to refine them followed by density modification. After density modification, I ran solvent flattening. Then I calculated the anomalous map using the phase from sharp and the electron density map from solvent flattening. The anomalous map shows the density around these 10 selenium sites are clear and round. However, the density map from solvent flattening showed that only 4 selenium sites have clear and round density.The density around these 4 sites clearly showed beautiful helices. surprisingly, other 6 selenium sites have poor density or no density at all. The electron density around them is not very good and the predicted helical density is flat. I check the electron density before I ran solvent flattening. The result is same. I am quite confused about the big difference from these two maps. I also try SnB to find the selenium sites. The solutions are same as those from ShelxD. But How to explain the poor density around the selenium sites in the density modification map? Is there any problem with my selenium sites? Any suggestion from crystallographic experts? Thanks. Mousheng Wu, PhD Center for Membrane Biology Department of Biochemistry and Molecular Biology The University of Texas Medical School at Houston 6431 Fannin Street, Houston, TX, USA, 77030
Re: [ccp4bb] Pseudo-symmetry/refinement
Would you please explain how to proceed for "rigid body refinement against weak reflection" & "normal restrained refinement against strong reflection".
[ccp4bb] coot color question
Hi, Is there anyway coot can color molecule backbone by diffrerent residue ranges specified by user? Any other directions for doing this in VMD will also be appreciated! Hailiang
Re: [ccp4bb] Pseudo-symmetry/refinement
Mike, You could try rigid body refinement against the weak reflections to get the position of the molecules right and then normal restrained refinement against the strong reflections. I had a case like this some years ago and that helped... Esko On 17.10.2010, at 6.48, Mike John wrote: Hi all, The data is 2.2A, p41212, unit cell has c axis twice longer than a or b. Data processed by HKL2000, the diffraction pattern shows Strong-weak-weak in C direction, indicating translational pseudo- symmetry. Xtriage analysis confirmed the pseudo-symmetry (large Patterson off- origin peak). The model is 100% identical searching prob. Phaser MR solved the structure easily with good Z-score and LLG(3 copies/a.u). The problem comes during the refinement: The R-free converged around 50% (R-factor 38%) and never go down even though I tried hard including, twin possibility. Seeking help to lower the R-free. Thank you very much Mike
