Re: [ccp4bb] About system absence in P4222?
Thank you Ian for the example - I hadnt thought of the effect of an NCS translation of (x,y,1/2) in higher than 2 fold symmetry.. Eleanor in Ian Tickle wrote: Hi Lijun, I take your point, and you're right I've confused someone else already! I made the NCS exact because a) I was using Eleanor's example (exactly) and was too lazy to make it inexact, and b) making it exact makes the point equally well as making it inexact (actually IMO better because it makes it very easy to distinguish pseudo-absences from accidentally weak reflections) - as long as you don't over-interpret the results! So for anyone who's confused, my apologies, just imagine that the NCS translation isn't exact, and consequently the 'absences' won't be exactly zero. The point I was making is that NCS translations do not necessarily produce the same systematic absences (or pseudo-absences) as crystallographic translations. Cheers -- IAn -Original Message- From: Lijun Liu [mailto:li...@uoxray.uoregon.edu] Sent: 15 December 2008 18:10 To: Ian Tickle Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] About system absence in P4222? Ian, Your examples may cause more confusion, especially for those beginners with symmetry. In your P222 and P3 cases, an exact NCS (0, 0, 1/2) turns to be an exact crystallographic translation, which reduces the unit cell to a half while the reciprocal unit cell gets doubled. A half of reflection were absent, including those listed as (0, 0, 2n+1). This rule applies generally to all non-centrosymmetric space groups (P1, P2, P3, P4, and P6) with P-lattice when only having one rotational symmetric element other than P1, and some other space groups like P222. (Pseudo) translational NCS' role in systematic absences(weakness) is complicated. However, to do the math with -- Plug the coordinates (x,y,z) and x+tx, Y+ty, z+tz) into the SF equation. -- is exactly the only way to test it. Lijun On Dec 15, 2008, at 5:04 AM, Ian Tickle wrote: But that only means that the SF contribution from that pair of molecules in the unit cell is zero for (00l) l=odd reflections. Depending on the crystallographic symmetry (e.g. if it were 3-fold or higher order) there may be other pairs for which the SF contribution is non-zero for all (00l) (but zero for the the odd orders in some other line that is symmetry-equivalent to (00l)). So for example I did a test with 2 mols in the a.u. related by an exact (0,0,1/2) NCS translation in P222: h k l Fcalc phicalc 0 0 10.00180.00 0 0 2 5120.88180.00 0 0 30.00180.00 0 0 4 1273.09 0.00 0 0 50.01 0.00 0 0 6 260.21180.00 0 0 70.00180.00 0 0 8 39.42180.00 0 0 90.01 0.00 0 0 10 43.19 0.00 0 0 110.00180.00 0 0 12 118.59180.00 0 0 130.01 0.00 0 0 14 120.89180.00 0 0 150.01 0.00 (00l) l odd are definitely absent here! - because none of the crystallographic 2-folds affect the (0,0,1/2) translation. Then I generated 2 mols in the a.u. related by the (1/2,0,0) NCS translation in P4 to get the (h00) line (note that the 4-fold along c would not affect a c-axis translation): 1 0 025189.10 0.00 2 0 0 200.09 0.00 3 0 014404.46180.00 4 0 012608.60180.00 5 0 0 4669.64180.00 6 0 0 748.81 0.00 7 0 0 3184.06 0.00 8 0 0 3858.87 0.00 9 0 0 2578.38 0.00 10 0 0 382.61 0.00 11 0 0 683.43180.00 12 0 0 444.89180.00 13 0 0 236.65180.00 14 0 0 352.46180.00 15 0 05.62 0.00 No absences! The 4-fold generates a pair of molecules related by the (0,1/2,0), not the (1/2,0,0) translation. So Eleanor is right only in specific cases, Ronald is right in the general case. As an aside, while I was verifying this, I think I found a problem with the P3 specific SF calculation in SFALL. Here's what I get for 2 mols in the a.u. related by an exact (0,0,1/2) NCS translation in P3 using the default P3 specific routine: 0 0 18.24 -175.63 0 0 2 7339.05121.46 0 0 3 27.32125.92 0 0 4 949.76-10.37 0 0 5 39.10 -103.39 0 0 6 461.79 -115.99 0 0 7
[ccp4bb] Recruitment in Structural Biology/Biophysics
Dear All, The College of Life and Environmental Sciences at the University of Birmingham is seeking to recruit a research group leader in structural biology or a related discipline. Individuals pursuing the study of structure-function relationships in the context of membrane transport or transmembrane signalling are particularly welcome to apply. Successful applications will be able to demonstrate research endeavour at the highest standing and a proven record of teaching at all relevant levels. Further details can be found at http://www.biosciences.bham.ac.uk/ NewAppointments/New_Appointments.htm. Informal enquiries should be directed to Prof. Kevin Chipman, Head of School of Biosciences, 0121-414 5422 or j.k.chip...@bham.ac.uk. - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ -
[ccp4bb] clapham, or ccp4 6.1.0 release
Dear All as we continue our journey up the A65 (towards the heart of Yorkshire) we are pleased to announce the release of Clapham (or 6.1.0). This is available form the usual locations http://www.ccp4.ac.uk/download/downloadman.php or ftp://ftp.ccp4.ac.uk/ccp4/6.1/ Obviously special thanks to the program authors, testers etc. Go enjoy New goodies: * REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous refinement (Garib Murshudov, Raj Pannu, Pavol Skubak). * PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD. * AFRO: multivariate substructure factor amplitude estimation for SAD/MAD (Raj Pannu) * BALBES: automated molecular replacement (Fei Long, Garib Murshudov, Alexei Vagin). * cBUCCANEER: statistical model building, optimised for experimental phasing. (Kevin Cowtan) * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan Abrahams) * CTRUNCATE: New program for Intensity to Structure Factor conversion and checking data quality (Norman Stein). * IMOSFLM: imported imosflm 1.0.0 * MrBUMP: Automated molecular replacement, search model retrieval and search model preparation for molecular replacement. * PARROT: automatic density modification and phase improvement (Kevin Cowtan) * PISA: the standalone version of the Protein Interfaces, Surfaces and Assemblies server. (Eugene Krissinel) -- optional * POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans) * RAPPER: conformer modelling through sampling residue rotameric states. (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty, Swanand Gore and Tom Blundell) -- optional * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan) * XIA2: Automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable for immediately starting phasing and structure solution. plus many updates including * CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu) * MOLREP: updated to version 10.2.12. * MOSFLM: updated to version 7.0.4. Please note that the downloads are large (very large if you include the balbes database), so there may be an issue of browsers timing out (observed for firefox so far). Charles Ballard on behalf of the CCP4 team.
[ccp4bb] superpose structures .ssm or lsq which is better
Dear All, I am overlaying several structures using coot. There are two ways SSM or LSQ can be used in that package. But I got clearly different result form the two methods. In my opinion SSM only works on the secondary structures and LSQ can works on the whole atoms ,main chain or CA. So the question is which one is better to overlay structures, LSQ or SSM ? Thanks a lot! liu
Re: [ccp4bb] generating omit maps
SFCHECK (method unknown) please see CCP4 documentation
[ccp4bb] disulphide refinement
Hi all, Can anyone tell me how to refine in Refmac a disulphide bond between symmetry-related molecules? Thanks in advance, Karolina
Re: [ccp4bb] clapham, or ccp4 6.1.0 release
We really appreciate all the efforts from the great CCP4 team. But I am sorry, there are no prebuilt executables for SGI IRIX6.5 now? There used to be such a bundle for the older versions. It's really a pain to do all the compilation which never go through smoothly. Shall we wait for such a bundle or we should start to struggle with the compilation right now? Thanks for your attention. Jie Liu Charles Ballard wrote: Dear All as we continue our journey up the A65 (towards the heart of Yorkshire) we are pleased to announce the release of Clapham (or 6.1.0). This is available form the usual locations http://www.ccp4.ac.uk/download/downloadman.php or ftp://ftp.ccp4.ac.uk/ccp4/6.1/ Obviously special thanks to the program authors, testers etc. Go enjoy New goodies: * REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous refinement (Garib Murshudov, Raj Pannu, Pavol Skubak). * PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD. * AFRO: multivariate substructure factor amplitude estimation for SAD/MAD (Raj Pannu) * BALBES: automated molecular replacement (Fei Long, Garib Murshudov, Alexei Vagin). * cBUCCANEER: statistical model building, optimised for experimental phasing. (Kevin Cowtan) * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan Abrahams) * CTRUNCATE: New program for Intensity to Structure Factor conversion and checking data quality (Norman Stein). * IMOSFLM: imported imosflm 1.0.0 * MrBUMP: Automated molecular replacement, search model retrieval and search model preparation for molecular replacement. * PARROT: automatic density modification and phase improvement (Kevin Cowtan) * PISA: the standalone version of the Protein Interfaces, Surfaces and Assemblies server. (Eugene Krissinel) -- optional * POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans) * RAPPER: conformer modelling through sampling residue rotameric states. (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty, Swanand Gore and Tom Blundell) -- optional * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan) * XIA2: Automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable for immediately starting phasing and structure solution. plus many updates including * CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu) * MOLREP: updated to version 10.2.12. * MOSFLM: updated to version 7.0.4. Please note that the downloads are large (very large if you include the balbes database), so there may be an issue of browsers timing out (observed for firefox so far). Charles Ballard on behalf of the CCP4 team.
[ccp4bb] RMSD's authority
Dear ccp4bb, Can anyone point me to a table/paper that gives acceptable RMSD's for bond lengths and angles against resolution? We have had two different referees for a paper contradict each other and I am not sure what to use as a good authority for this. Thanks, Simon
Re: [ccp4bb] RMSD's authority
bond angle an length rmsd is a completely context sensitive data item. It can be zero (for torsion angle refinement with fixed bonds and angles) up to the same rmsd values observed for small molecule targets. Anything in between is fair game, with the general tendency to become larger with more relaxed restraints (i.e. more data). So it depends on your refinement protocol and restraint settings. Asking for certain hard rmsd values that match all refinements is old school, despite what some references might tell. Ian will probably expand more about the relation to maximum log free likelihood. Best check his Acta D papers on that subject. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Simon Kolstoe Sent: Tuesday, December 16, 2008 9:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] RMSD's authority Dear ccp4bb, Can anyone point me to a table/paper that gives acceptable RMSD's for bond lengths and angles against resolution? We have had two different referees for a paper contradict each other and I am not sure what to use as a good authority for this. Thanks, Simon
[ccp4bb] Young Crystallographers Group
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Re: [ccp4bb] RMSD's authority
Hi Simon I think I can say without fear of contradiction that this is still a subject under debate, so I'm not at all surprised that the referees can't agree between themselves! I think there are actually two answers to your question: (1) what is the formally correct answer, and (2) what is the answer that should be acceptable to a referee who is open to reasoned argument. In many ways it's easier to give answer (2), since answer (1) is not yet settled in a way that is easily usable. The first thing I should point out is that you definitely won't find a table/paper that gives acceptable RMSDs for bond lengths and angles against resolution, so don't bother looking for one, sorry! If you want the 'CCP4 community view' on this I think I can speak for the majority and say that a reasonable compromise is to take the median value of RMSD(bonds) (originally suggested by Clemens Vonrhein I think - as least that's the value I use if I have to choose one) to use as a target in refinement at 'typical' resolutions (say between 2.5 and 1.5 Ang). I think it is generally accepted now that the RMS Z-score (Z=deviation/SD)is a more statistically meaningful value to quote (printed by the latest versions of Refmac), so since the range of RMSZ(bonds) values is by definition 0 to 1, the median is 0.5, which corresponds to a RMSD(bonds) of about 0.012 Ang. For bond angles the corresponding values are RMSZ(angles) ~ 0.75, RMSD(angles) ~ 1.5 deg. Having said that, my view (as set forth in Acta Cryst., 2007, D63, 1274-81) is that the correct target for optimisation of weights is not RMSZ/RMSD(bonds) at all but Rfree (as originally suggested by Brunger), or better the log(free likelihood) (suggested by Bricogne). If you do that (properly) the evidence is that do you get resolution-dependent values of RMSD/RMSZ, i.e. lower values at lower resolution, and higher values at higher resolution than the 'typical' resolution range indicated above. For example CNS/CNX and phenix.refine (I believe, though I can't vouch for it as I don't use it), which do implement weight optimisation 'properly' using Rfree as the target, often gives RMSD(bonds) ~ 0.006 (RMSZ ~ 0.25) for resolutions around 2.5 Ang or lower. Also Shel-X seems to give sensible resolution-dependent RMSD/RMSZ(bonds) values (though not for angles, since it doesn't parameterise the uncertainties using the Engh Huber values). Sorry if this doesn't give the definitive answer you were looking for, but I hope it helps to convince the wayward referee! Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Simon Kolstoe Sent: 16 December 2008 17:51 To: CCP4BB@JISCMAIL.AC.UK Subject: RMSD's authority Dear ccp4bb, Can anyone point me to a table/paper that gives acceptable RMSD's for bond lengths and angles against resolution? We have had two different referees for a paper contradict each other and I am not sure what to use as a good authority for this. Thanks, Simon Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] O/T: microscopes
Hi, I am looking to buy a modestly-priced zoom scope for x-ray crystallographic purposes ($2-3000). Does anyone have suggestions about what/where to possibly find this? I currently have a cheap one that goes from 7.5-50X, but I'd like something with a little more magnification, a better light source and better optics. Thanks, Clint Clint Spiegel Assistant Professor, Chemistry Western Washington University 516 High Street Bellingham, WA 98225-9150.
Re: [ccp4bb] O/T: microscopes
Clint, We have a Leica MZ125 scope with a Leica KL1500 LCD lightsource. It has adjustable zoom from 8x to 160x with the 16x occular lenses but can do up to 640x with a different occular. We also opted for the optional optical micrometer and polarizing lenses for looking at birefringence. Additionally, they sell an attachment for hooking up a digital camera to take pictures of your crystals. This scope went for about 8k or so a year ago which is a little more than you're looking to spend but the optics are great and it beats out any scope I've used thus far even though I've only been doing crystallography for 4 years. Cheers, Jim On Tue, Dec 16, 2008 at 2:00 PM, Clint Spiegel spie...@biology.ucsc.eduwrote: Hi, I am looking to buy a modestly-priced zoom scope for x-ray crystallographic purposes ($2-3000). Does anyone have suggestions about what/where to possibly find this? I currently have a cheap one that goes from 7.5-50X, but I'd like something with a little more magnification, a better light source and better optics. Thanks, Clint Clint Spiegel Assistant Professor, Chemistry Western Washington University 516 High Street Bellingham, WA 98225-9150. -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
