Re: [ccp4bb] H32 use
I thought H 32 was a PDB requirement? CCP4 programs take a belt-and-braces approach - read the symbol but also check the cell dimensions and set up symmetry accordingly.. But it is a pain if headers are inconsistent with PDB deposition requirements - des anyone know more details? Eleanor Bernhard Rupp wrote: Dear All, I wonder whether it is a good idea to still accept H32 as a space group in the PDB CRYST1 record, despite it may be used internally by programs. * The combination of hexagonal cell parameters and R32 clearly indicates a hexagonal (obverse) axis setting in the R centered cell. * The H-M R32 symbol with rhombohedral setting a, alpha, is inconsistent anyhow because the cell is then primitive and not centered. * The ITCA (and most data mining programs?) seem to be unaware of a Bravais symbol H. The practice of using H32 anywhere in published data should be strongly discouraged. Internally please feel free to use whatever works. What is the current opinion on this? Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] buster-tnt on OSX ?
Clemens Vonrhein schrieb: ... A nice task would be to compare different integration/scaling packages at various stages: for finding the sites e.g. in SHELXD and separately (using known sites) for giving best phases e.g. in SHARP. there could be differences. Yes, maybe it is finally time to get past the rumour stage of software comparison. The only way I can think of is to start with a standard set of data that cover the range of typical experimental situations. The Quality Control article in XDSwiki ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control ) is meant to enable users and developers to do exactly what Clemens proposes. Users/developers can download the datasets that this article talks about, and run them through their favourite data reduction program(s), and report the results in new articles linked to the Quality Control one. But one word of warning: comparisons of complex pieces of software are not entirely straightforward; e.g. different people may obtain different results with the same software package, and different versions of the same software may behave differently. So this is a never-ending project. Nevertheless I do believe that one can learn a lot about using software in the right way, for a given project, and generalize from that. best, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilites, please ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] Comparison of Integration Programs (was: Re: [ccp4bb] buster-tnt on OSX ?)
Hi Folks, The idea of comparing different data reduction packages is an interesting one. It is not however without challenges as alluded to by Kay. As far as I can see there are two main challenges - the first is that different users when given the same tools will do different things - in challenging cases this will be very significant [Kay's point]. The second is to be able to express why a given package did better than others for a specific case, then bootstrap your way back to some general rules (i.e. expertise) about the packages for future reference. For a single case this was looked at in (ahem): Acta Cryst. (2007). F63, 168-172 Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489) C. Meier , L. G. Carter, G. Winter, R. J. Owens, D. I. Stuart and R. M. Esnouf Where we concluded that XDS did a better job than Mosflm or Denzo because the mosaic spread was rather high and the oscillations a little narrow. We did not try d*TREK but I would anticipate it would work well as the method of integration is similar to XDS. The better job in question though was to give a data set which would give a refinable molecular replacement solution, where the others did not. Now something which I have been interested in doing but which is almost certainly prohibitively expensive in terms of time is to take a number of data sets of varying levels of challenge and get the program authors (or delegated experts) to do their absolute best with the data reduction with that program, then compare the results. This will help to reduce the impact of lesser known but very helpful options (i.e. outlier recycling in XDS CORRECT, say) and perhaps generate a more fair comparison. In the example above there may have been some tweaks which could have been made to improve the results substantially for the 2D integration packages. For most (easy) cases however the best tool for the job is the one you know best. If you have the spare CPU horsepower and time, you can always reduce the data with all available packages and see which one gives the best results for your case - something which would be perfectly reasonable for substructure determination but much more unusual for data reduction. From my testing of xia2 against structural genomics data I can say that, for easy data, there is not much to call between Mosflm / Scala and XDS / XSCALE. Just my 2c. Cheers, Graeme
Re: [ccp4bb] about the PEG molecules in crystals
Dear Jiamu! Have a look at http://dx.doi.org/10.1524/zksu.2006.suppl_23.613. It might help you. Regards, Dalibor -- Dalibor Milic Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-1 Zagreb Croatia phone: +385 1 460 6377 fax:+385 1 460 6341 e-mail: [EMAIL PROTECTED] On Uto, listopad 28, 2008 11:14, Jiamu Du wrote: On Tue, Oct 28, 2008 at 4:55 PM, Boaz Shaanan [EMAIL PROTECTED] wrote: Hi, I'm not sure what you're after but PEG molecules at various length have been described in many structures deposited in the PDB. I can point you to two of ours, 2f1f and 2pan but there are many others, as I said. I don't know what's there to discuss. It's either you see their density and fit them or you don't. Cheers, Boaz - Original Message - From: Jiamu Du [EMAIL PROTECTED] Date: Tuesday, October 28, 2008 7:45 Subject: [ccp4bb] about the PEG molecules in crystals To: CCP4BB@JISCMAIL.AC.UK Dear all, Dear Boaz, The situation is that I co-crystallized a protein with a peptide. The binding cleft of the protein is pre-occupied by a PEG instead of the peptide. So, I want to searching some article to see how to deal with it and if there is some implication from the artificial complex. Are there some articles or reviews discussing about the PEG molecules in crystals or the biochemical features of PEG? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [EMAIL PROTECTED] Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaananý -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] H32 use
Seems to me the sensible approach is the systematic H-M symbol defined in syminfo.lib, i.e. the first letter is always the centring symbol (PIRFABCH) and then if there's any ambiguity the basis can be indicated with a : appendage, so R3:H or R3:R etc, then H3 et al is reserved for H-centred P3 et al. In reality there is never any ambiguity between R3:H and R3:R, as you said it's always obvious from the cell which is the appropriate basis. I've learned from bitter experience never to trust the SG symbol anyway! - if it's R3, R32, H3, H32 I always test the cell and reset the symbol if necessary! If anyone starts using H centring that will break my code since I can't distinguish between H3 (PDB) and H3 (IUCr): they can't of course since H centring is (thankfully) never used in syminfo.lib. But as you point out there is still the potential for confusion in publications. Historically I believe that R3 was first defined as the hexagonal basis with R centring, which would be logical. Then later on some crystallographers decided they preferred the primitive rhombohedral cell with the 3-fold along the body diagonal; logically this should have been called P3, except that the name was obviously already taken, so they continued to call it R3 even though it was P not R centred. This was perhaps not such a good idea in hindsight. So historically the vast majority of crystallographers used R3 to mean R3:H, and only a small minority ever actually used it to mean R3:R (for a long time most software never supported the latter option anyway, maybe a lot of it still doesn't). So it's unfortunate that the PDB's change from R3 to H3 inconveniences by far the largest group of users! - so I think remedying the historical mistake of using R3 to mean primitive rhombohedral cell by making it R3:R (or maybe P3:R would be more logical), and keeping with R3 for the R centred, hexagonal obverse basis would have been wiser! The other big inconvenience that was thrust on us was of course the possibility that SG names could contain spaces. The pain that this caused was totally unnecessary because the original set of SG symbols without embedded spaces were already unique, even if you threw the additonal set of long symbols (e.g. P1211) in with the short ones (P21). Even if the issue was merely one of legibility (P 1 21 1 is slightly easier to read), this could have been handled by mapping internally stored versions without spaces to the user-visible versions when printing log files etc. -- Ian -Original Message- From: Bernhard Rupp [mailto:[EMAIL PROTECTED] Sent: 28 October 2008 05:22 To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] H32 use Good point. Btw, also these nonstandard, triple ab-plane centered H3x cells can be readily reindexed standard primitive, so no new space groups are needed...let's not give the PDB new ideas... BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: Monday, October 27, 2008 7:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] H32 use In fact there's another good reason not to use H3 etc when you mean R3: the H lattice symbol is already in use to mean something completely different! - namely H-centring in *trigonal hexagonal* (i.e. *not rhombohedral*) space groups such as P3, P3/1 etc supergroups, so e.g. H3 is actually a supergroup of P3 not R3. See here: http://books.google.co.uk/books?id=ilVvOYOFCx8Cpg=PA96 and here: http://img.chem.ucl.ac.uk/sgp/large/trigonal.htm and the above is consistent with the definition now adopted in the new ITC-A1: http://it.iucr.org/cgi-bin/itsearch?query=DC.creator%3D%22H.%2 2%20AND%20 DC.creator%3D%22Wondratschek%22metaname=swishdefaultIT.group =2.1.4IUC r.volume=A1 It would be interesting to know if the PDB consulted the IUCr on this change! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 27 October 2008 22:50 To: CCP4BB@JISCMAIL.AC.UK Subject: H32 use Dear All, I wonder whether it is a good idea to still accept H32 as a space group in the PDB CRYST1 record, despite it may be used internally by programs. * The combination of hexagonal cell parameters and R32 clearly indicates a hexagonal (obverse) axis setting in the R centered cell. * The H-M R32 symbol with rhombohedral setting a, alpha, is inconsistent anyhow because the cell is then primitive and not centered. * The ITCA (and most data mining programs?) seem to be unaware of a Bravais symbol H. The practice of using H32 anywhere in published data should be strongly discouraged. Internally please feel free to use whatever works. What is the current opinion on this? Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL
Re: [ccp4bb] about the PEG molecules in crystals
biochemical features of PEG? They give you the runs. http://en.wikipedia.org/wiki/Polyethylene_glycol BR
Re: [ccp4bb] buster-tnt on OSX ?
Gerard, Thank you very much for clearing that up. It's always good to hear that there's one less things I need to worry about. Pete Gerard Bricogne wrote: Dear Pete, Thank you for your message. I can confirm that you need not worry about this clause: it is meant to prohibit the aggressive use of code decompilers with the intention of stealing the content of the source code. What you have described in your hypothetical example is nothing of the sort, but instead a very useful kind of comparative evaluation. With best wishes, Gerard. -- On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote: Apologies for going slightly further off-topic... Last time I had a free half-day to look into sharp, I noticed that the academic license prohibits reverse-engineering. This seemed to put any comparative testing into a slightly grey area. For example, if I find that sharp does the best job refining sites, but bp3 outputs better phases for a dataset due to different representation of phase probabilities*, I've implicitly constructed a primitive model of how sharp is working. This seems close enough to a first step of reverse-engineering that I was concerned. Could someone confirm that I'm worrying about things I don't need to here? Pete * Purely hypothetical example.
Re: [ccp4bb] SUMMARY refmac newligand noexit?
Looks like this was a combination of new atom names, and using on older version of refmac. Thanks to Garib, a combination of using the new dictionaries and refmac 5.6 does the trick. Pete Pete Meyer wrote: Thanks for the quick reply. I got the noexit option for the ccp4-6.0.2 html, so you might have already started adding it. I've had no luck with 5.2.0019 (ignores either keywords, stops with new ligand message) and 5.4.0077 (ignores noexit, fatal error for continue). I'll give it a try with the latest 5.5 version. Thanks again, Pete Garib Murshudov wrote: The keyword is make newligand continue (I need to add noexit option. It makes sense) regards Garib On 26 Oct 2008, at 22:10, Pete Meyer wrote: Hi, I'm attempting to use refmac to re-calculate a map from a published structure. Most of the time, this works with no problems. Occasionally, refmac stops with New ligand has been encountered. Stopping now. From the manual, I'd though that using MAKE NEWLIGAND NOEXIT should prevent this, but that doesn't seem to be the case. Any suggestions for working around this? Pete Garib Murshudov http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Erice 2010: Structure and Function from Macromolecular Crystallography: Organization in Space and Time http://www.crystalerice.org/erice2010/2010.htm
