Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"
The replacement of the EDS might be an excellent opportunity to upgrade/include the newer EDSTATS metrics and make these raw data also downloadable/parse-able for analysis purposes (xml). A server option where you can send in your own PDB files (included in the validation server?) before submission might be useful (the current ccp4 implementation of EDSTATS fails to convince)...the effect of the deterrence experiencing public maps/stats looking as bad as the ones dreamt up at home might enhance deposition quality. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Tuesday, December 13, 2016 9:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant" Hi all, After tirelessly serving the scientific community with (mostly) beautiful maps for two decades, the Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is now reaching the end of its life (in fact, it has been living on borrowed time for several years already). Some time in 2017 it will therefore be "phased" out and join the choir invisible (despite its beautiful plumage). The good news is that much of the EDS functionality (and in particular the delivery of map and mtz files, as well as a much better 3D viewer) is now provided by the Protein Data Bank in Europe (PDBe; http://pdbe.org/). There is a short write-up that explains what this means for users who just want to look at maps, for users who want to download files, for users of software that retrieves data from EDS, and for developers of such software (incl. URLs for map, mtz and other relevant files on the PDBe website) at: http://www.ebi.ac.uk/pdbe/eds Toodle pip! --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let "z" be the radius and "a" the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] diffraction images simulator
Contact James Holton, he has MLFSOM and other goodies. James Holton (jmhol...@lbl.gov) Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniele de Sanctis Sent: Friday, November 25, 2016 8:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] diffraction images simulator Hi all, I need to simulate some diffraction images and play with different parameters (divergence, flux, bandwitdh, beamsize, crystal size, ...), and I was wondering what are the most up-to-date available software . Thanks for your help Daniele -- ἀρετή --- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869
[ccp4bb] Model parts rearrangement
Hi Fellows, I seek advice for a trivial but tedious problem: I have rebuilt, automatically and manually, several parts of a structure, which of course, are all over the place in different ASUs. I also have a reference model, where the parts form a correct ASU. Is the a program/script that can accomplish this assembly of parts onto the correct model given the reference model? This is probably a common nuisance with a tool already available. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - The man who follows the crowd will get no further than the crowd. The man who walks alone will find himself in places where no one has been before. -
Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
Once more to those who feel offended by the structures in discussion: I’d be very careful at judging low resolution structures. This is a tricky business requiring a lot more info than just the PDB validation report. The 3+ to 4 A resolution range is a particularly deceptive one: The crystallographer does not have much data given the model parameters (perhaps consulting his figure showing determinacy for coordinate refinement might help) http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-11.htm At this resolution one has about enough data to keep enthusiasm up but at the same time it is not quite yet bad enough to throw up the hands and admit that that one is de facto modelling with a few X-ray restraints (i.e. data), requiring correspondingly suitable refinement protocols (and discipline, aka mental restraints in addition to stereochemical restraints). One is easily spoiled by looking exceptional 2A structures of huge complexes, but nature (I do not mean the journal but the same time would not exclude it) is often cruel. Particularly in Molecular Replacement structures, and here particularly in those with multi- segment/domain models, there are almost always parts that fit well and others that fit poorly - with simply not enough data at the given resolution to improve the poor parts sans additional phase information. Bias issues have been discussed and need not be iterated here. Pavel is correct in pointing out that a model with better geometry is also a more plausible model. What we cannot tell sans supporting density is whether it is a more accurate model, although I have rarely seen an improvement in geometry giving worse density fit. Usually a mess remains a mess - there is (at this resolution) no free lunch. The key question is again – does the model justify the specific conclusions drawn from it? If a poor model is better than no model at all, be it, as long as this is recognized and not used as an excuse for careless work. Facile dictu, difficile factu. Best, BR For every sufficiently complex problem there is an answer that is simple, clear and wrong. LH Mencken From: Narayan Viswam [mailto:nvisw...@gmail.com] Sent: Monday, April 27, 2015 12:02 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers! Sorry can't help it. The aggressive replies are mainly from senior PIs from US - friend in need is friend indeed.
Re: [ccp4bb] PAD images
Thanks - particularly great if we had these images/option available to look at in real time during data collection, w/o first having to download the raw data (not really feasible during remote data collection). I don't think the ESRF online data base has the option, but other beam lines may? Thx, BR -Original Message- From: James Holton [mailto:jmhol...@lbl.gov] Sent: Monday, April 27, 2015 4:05 PM To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PAD images In the ADXV viewer: http://www.scripps.edu/tainer/arvai/adxv.html Go to Edit:Settings and click on the Small Spots radio button. This solves most of the I can't interpret the spots problems you describe. -James Holton MAD Scientist On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Hi Fellows, I wonder whether it's just me and my eyesight failing (or excessive internal lubrication) It seems that the art of looking at diffraction patterns and being able to tell a lot about modulation, superstructures, extinctions, etc. becomes kind of useless old fart stuff when dealing with PAD images. I can't for my life see interpretable patterns on frames where the beamline autoprocessing delivers actual data sets. The absence of a point spread function etc that gave interpretable film-like images on IPs or CCDs, seems to be the reason. A PAD pixel with 100 counts looks like one with 100 when viewed with the low dynamic range of the displays compared to the huge dynamic range of the detector. Is there somewhere in the process a humanly unusable composite image with a point spread that allows visual pre-processing, inspection, and interpretation despite a low dynamic display range? Looking at the hklview or similar after processing is pointless (no pun intended), because the stuff I might be interested in is already processed away. Some humanly interpretable raw data images would be quite useful... Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org http://www.ruppweb.org/ - The man who follows the crowd will get no further than the crowd. The man who walks alone will find himself in places where no one has been before. -
[ccp4bb] PAD images
Hi Fellows, I wonder whether it's just me and my eyesight failing (or excessive internal lubrication) It seems that the art of looking at diffraction patterns and being able to tell a lot about modulation, superstructures, extinctions, etc. becomes kind of useless old fart stuff when dealing with PAD images. I cant for my life see interpretable patterns on frames where the beamline autoprocessing delivers actual data sets. The absence of a point spread function etc that gave interpretable film-like images on IPs or CCDs, seems to be the reason. A PAD pixel with 100 counts looks like one with 100 when viewed with the low dynamic range of the displays compared to the huge dynamic range of the detector. Is there somewhere in the process a humanly unusable composite image with a point spread that allows visual pre-processing, inspection, and interpretation despite a low dynamic display range? Looking at the hklview or similar after processing is pointless (no pun intended), because the stuff I might be interested in is already processed away. Some humanly interpretable raw data images would be quite useful... Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org http://www.ruppweb.org/ - The man who follows the crowd will get no further than the crowd. The man who walks alone will find himself in places where no one has been before. -
Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
Well, with full respect to your sensitivities as far as your own person is concerned: if you play rough (and 5 exclamation marks qualify by commonly accepted email etiquette as incipient flame, at least), you need to be willing to take a few as well... Best, BR - Trigger warning --- This message may or may not contain references to issues of privilege and oppression in- cluding but not limited to enantiophobia, point classism, heteroatomism, transbondism, cisbonding, sizeism, curvature, references to color, alcohol, blood, small insects, cancer cells, and any combination thereof that may cause symptoms ranging from discomfort and anxiety to violent physical response in sensitive individuals and must therefore be labeled as potentially hazardous to your comfort and well-being. - Trigger warning --- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Misbah ud Din Ahmad Sent: Thursday, April 23, 2015 2:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers! I feel rather uncomfortable and cornered with the aggressive replies and phrases like throwing stones, public humiliation etc., which suggest that I have some personal enmity with the author. The structure is in the public domain and questions can be asked about it. I as a beginner in crystallography learn from each discussion on this board and such harsh and insinuating responses may, in future, deter people like me from posting any questions at all and learning refinement strategies like the one which Pavel outlined to improve such type of structures. Best Misbha On Thu, Apr 23, 2015 at 9:17 PM, Gert Vriend gerrit.vri...@radboudumc.nl wrote: At around 4.0 A resolution one normally cannot talk about accuracy. The density will at most locations not warrant any detailed interpretation. If, at 4.0 A resolution, you move atoms around a bit, you will not see significant changes in R/Rfree. So, you can do whatever you want, more or less. If the refinement puts great emphasis on the secondary structure (i.e. tries to force the Ramachandran plot, then you get a good Ramachandran plot, but if they put more weight of the fit to the density, you get a slightly lower R (and perhaps even Rfree) at the cost of the Ramachandran plot. And all of that is meaningless. At this resolution you have to check if the fold is likely to be correct. I superposed just any high(er) resolution domain with high sequence similarity at the corresponding 3bdn domain, and I take any bet that the fold of 3bdn is right (at least of the domain I looked at, and I extrapolate to the other domain). PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/) cannot improve this one, and WHAT_CHECK (http://swift.cmbi.ru.nl/gv/pdbreport/) throws its hands up in the air. At 4.0 A you should be happy with an indication of the fold (and with the fact that the authors probably went through great pains for you getting these coordinates close to where they should be). Gert
Re: [ccp4bb] funding experiences - query
Hi Fellows, thanks to all who have responded to my query. The response were very elucidating, and at the same time (a) consistent and (b) depressing, even for my slightly cynical standards As no good deed goes unpunished, I wonder whether the respondents (and anyone else) have a reasonable idea how much resources and/or money/fte allocated to each project they spend (relatively is enough) from (a) conception to data (bioinfo, cloning variants, expression screening, scale-up, purification, crystal screening, mounting, data collection) compared to (b) data to structure (including analysis and validation). It is relatively easy to get agency funding numbers, funding success rates etc, but those break-up data are elusive, which is probably due to the fact that we re-engineer and divert a lot from other sources to get the prelims... Many thanks again to everyone for responding. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - Physicist are there to find the laws of nature. Engineers are there to work around them. -
[ccp4bb] funding experiences - query
Hi Fellows, hopefully everyone has recovered from the Easter Egg coma April jokes by now. Now something serious: for a commissioned opinion piece in a vanity journal, I seek to get a better understanding regarding improvement of review and funding decisions for crystallographic studies. Under assurance of full confidentiality, I would hope to hear from some of you off board comments/experiences on subjects/questions like those: Were you denied funding for a structure study because you did not have yet (a) large scale protein expression (b) first crystals (c) diffraction crystals (d) data (e) maps Did you have to 'reverse engineer' an application, i.e. you had the structure already (almost) and then write the grant? Any other peculiarities/comments you received, and what you feel would need improvement/should be addressed. Again, any comments will be confidential and will contribute to raise awareness for the special requirements of, and funding for, the significant up-front work necessary for crystallographic studies. Get it off your soul and make the world a better place. Thanks and best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers ---
Re: [ccp4bb] Picking water molecules at 4A structure.
Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Your question is justified in intent, but ill phrased. The question you are faced with is “How plausible would the assignment of a given electron density reconstruction feature as a water molecule be?” The answer depends on observational evidence and chemical plausibility. You have the most knowledge about your protein complex and should have some knowledge about chemical plausibility of your proposal. (a)A few questions to consider re. evidence: What is the noise level in your map? How do normal 2Fo-Fc densities compare to difference densities? Density shape? Other isolated mystery density of same levels somewhere? If your maps are excellent and low noise it is not impossible to see a very well bound water molecule at 4A. (b) Plausibility based on prior expectations: Was Mg in the cocktail? Being isoelectronic with HOH (and a favorite companion of DNA in crystallization), it might be a plausible candidate. Anything else heavier, perhaps? SO4, PO4? Perhaps any clues from anomalous data/ano diff maps? Fragments of PEGs? What does the refinement tell you? How did you refine? Does your protocol match the low resolution of the data? Even at the low resolution, do bond length and coordination support a discrete moiety? Distances, geometry, B-factors? If everything points in your favor, you can justify the proposition of a discrete moiety. Your scientific credibility depends on how well your proposition is supported by reasoning from (a) and (b) – probably with heavy emphasis on (b) as you are poorly determined – and not whether you are ultimately right or not. Although I doubt that a water molecule without biological relevance assigned to it has any effect on global refinement stats nor on your career, you can always invoke the rule of parsimony for your model – no explanation is better than an unsupported one. “I don’t know” is a perfectly scientific answer. LGBR
Re: [ccp4bb] Number of Molecules in Asymetric Unit
New kernel version http://www.ruppweb.org/mattprob/default.html http://www.ruppweb.org/mattprob/default.html Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of amro selem Sent: Wednesday, April 01, 2015 8:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Number of Molecules in Asymetric Unit Dear CCP4 Community , which program i should use in ccp4 backage to find how many molecules in Asymetric Unit . All the best Amr
[ccp4bb] Manuscript PRL
HI Fellows, just in time for some easy Easter reading, the first page regarding some new ideas about nucleation Link to full content is in the PDF document. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers --- Rupp_2015_Phys_Rev_Letters_114(13)_Tunneling_p1.pdf Description: Adobe PDF document
Re: [ccp4bb] Basic Anomalous Scattering Theory
A look at the term scheme might help to understand the absorption edge structure - pp 286 and Figure 6-30 BMC. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Wednesday, March 11, 2015 9:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Basic Anomalous Scattering Theory Dear Crystallographers, I have had only a vague understanding of what specific things are happening with shell electrons at anomalous edges. Specifically, for example, to what energy of electron-transition does the x-ray k-edge correspond in terms of orbitals, and is that transition energy actually equal to the energy of the photon, suggesting that the photon is absorbed (or disappears?) in elevating the electron? I don't think we say it is absorbed, so how does the energy come back out, from the electron's falling back down, right? So then there's a new photon created, or the same one comes back out? Where was it? Further, I also have heard that the emerging anomalous/resonance photons are of the same wavelength as the incident radiation, but usually there is something lost in transitions (even non-fluorescence ones) I thought? Has it ever been definitively shown that the anomalous photons are of the same energy as the incident radiation? In the case of L-edges, why are there three separate edges? Further, if the resonance occurs when the energies are equal, why does resonance occur at energies greater than the edge? I don't think this happens in other resonance phenomena, or does it? If projects a middle-C-tone into a piano, do all of the lower notes resonate as well, according to the Kramers-Kronig relation? I think it may actually happen in the mammalian cochlea's travelling wave, but is it completely general to resonance phenomena? Just interested, and have wondered these things for a long time in the background of my mind... Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] Twilight 2014 update
Dear All, Chris Weichenberger just released the 2014 update for TWILIGHT. It is available from my web site http://www.ruppweb.org/twilight/default.htm http://journals.iucr.org/d/issues/2013/02/00/issconts.html http://journals.iucr.org/f/issues/2013/02/00/issconts.html Please note: The list can be sorted by various scores, but all have their limitations. RSCC is a good start, but does not tell everything and does fail in various situations. One has to examine and investigate each case on its own merits. We do not provide any comments or analysis beyond the statistics RSCC, OWAB, and a total score. The most common reason for a bad score seems to be modelling with too much enthusiasm. Even if a part of a ligand fits very well, when the remainder is insouciantly added, the score will get hammered. This again points to the unresolved question what to do with parts of any moiety not completely visible in density.. Sans Souci may work for palaces, less so for ligands. Best wishes, BR
Re: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Sacha, I was imprecise. With unplaced I meant neither rotated nor translated. Once you become post-rotationally SF based, you can in fact compute a F(env) whole inclusion should improve the TF score. What is not evident to me is how to use a mask and compute the Fs if the orientation (rotation) is yet to be determined? Thx, BR From: Alexandre OURJOUMTSEV [mailto:sa...@igbmc.fr] Sent: Dienstag, 3. Februar 2015 22:19 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Bulk solvent correction in Phaser MR LF Dear Bernhard, For the unplaced model, it can only be a Babinet model to improve the scaling, This is not fully true, and the flat mask correction can be used as well. Please look : Fokine, A. Urzhumtsev, A.G. (2002) On the use of low resolution data for translation search in molecular replacement. Acta Cryst., A58, 72-74 Fokine, A., Capitani, G., Grütter, M.G. Urzhumtsev, A. (2003) Bulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNS. J. Appl.Cryst., 36, 352-355. Best regards, Sacha Urzhumtsev _ De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Envoyé : mardi 3 février 2015 14:49 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR
[ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR
[ccp4bb] [OT]:Typoglycemia
Today, after 6 years in circulation, John Tesmer kindly informed me about a labelling error in BMC figure 6-17 http://www.ruppweb.org/Garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-17.htm I think the reason that nobody has noticed it until now is perhaps (in addition to the fact that the just-put-it-under-the-pillow trick might not work as well as advertised) a case of crystallographic Typoglycemia: http://en.wikipedia.org/wiki/Typoglycemia Amzanig huh? Yaeh and you awlyas thguoht slpeling was ipmorantt. Cheers, BR k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo Vista, CA 92084 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
Re: [ccp4bb] chloride or water
After reading this exchange, I think at the core of the dispute is the question what a structure model really is supposed to represent (a), and how to annotate/describe it (b). ad (a) In general, and forgive me for not disclosing all caveats and fine tune (I leave this to GB), we are interested in the posterior likelihood (model likelihood). The two terms to consider (yes, I know, I am omitting any normalization necessary for hypothesis testing etc) this model likelihood would be proportional to the product of an evidence term (data likelihood) and an independent prior knowledge term. Imho the expressed opinions diverge primarily in the relative significance of the terms or normalization of the probabilities. The evidence purists (and it seems that computationalists often mistake this for arrogance of the crystallographers) argue that if I can’t see/recognize it in ED or support it otherwise by direct experimental evidence, leave it out of the model (after all, X-ray structure models are supposed to be based on experimental evidence). On the other hand, from prior knowledge (admittedly extracted from polluted data bases like the PDB and that is not meant as an insult but a statement of fact) we do know something about what reasonably could be expected and could use it to the full extent of its statistical support. Both extremes are of course justifiable, but in practice not separable. E.g. we use riding hydrogens without giving it a second thought that we do not see them in (macro X-ray) ED, and they do improve models. On the other hand, we still put side chain atoms we do not ‘see’ in specific positions and hope that the B-factors increase to a point where the absence of any meaningful scattering contributions does not ruin our Holy R. That specific position is perhaps closer to ‘wild speculation’ than the probability that a chloride atom exists in that specific case. (I do argue that in the above case a set of conformations with occupancies of rotamers corresponding to their population in the torsion angle landscape (or in the polluted databases) – the prior – under consideration where they cannot be – the rest of the model as obtained from evidence – would be a possible description). The final weighting one could apply might be a less tangible factor – how badly does it matter? If a ligand in a specific pose is modelled and intended for the use of drug discovery, I’d say the claim is extraordinarily strong, and the model likelihood (both terms) better be convincing. In the less earth shaking blob case, considering priors and the mentioned restrictions of low resolution etc, I can accept a low but not unreasonable probability (- such apparent evasiveness being a dead giveaway of a mental Bayes factor calculation instead of adherence to an artificial significance level; frequentists please feel free to flame me) for Cl as the most probable in the Cl/water/empty model competition (not that any of the models are overly convincing, however, compatible with the low drama factor of that decision). ad (b) having said this, how to express such probabilistic considerations in the current atomic PDB model format, is an unresolved issue. I think the whole idea of the single static atomic model sooner or later will fall. It is already a mess because much information about the model is hidden for example in remarks like TLS groups (btw, one of the most abused and ad-hoc applied means in the hope of reducing Holy R instead of reflecting what these groups actually mean). But this is besides the original point and becoming free floating… I am not calling for making peace here, rather argue that the seemingly insignificant issue of a single Cl ion in one of 100k structure models can lead to productive reflection about meaning and improvement of model description. Sorry for offending those in need for cozy comfort closing quotes. The answer is, as always, 42. HTC, BR (Happy To Confuse) From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Mittwoch, 21. Januar 2015 19:18 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water I reiterate that assigning a chloride is not “wild speculation” or “just making something up” in light of what we know about the situation. I see your point about not knowing that it’s a chloride, but I think you would agree that it is certainly more likely a chloride than map-noise, and perhaps more likely than water as well. Would you agree that chloride is the best guess, at least? What are the options for that blob, and what is the probability of each? I think you want to make sure people don’t get misled by it, which is a good point and a noble aspiration. I would argue that “not choosing” is here, as everywhere else, indeed choosing. And if you choose nothing here, you are almost certainly wrong, given
Re: [ccp4bb] CCP4 Release 6.5
OK I tried this on a 3rd machine (6.4 to 6.5 w/o uninstall of 6.4 before 6.5 install). Same result. Window attached. Somehow it seems the shortcut icon does not properly update. Its command becomes C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl Changing the command to C:\CCP4\ccp4i.bat fixes the problem. Attached as ccp4i.fat (to fool the mail attachment police). Maybe the attached info helps. 3x seems to show a patternthe only constant is me so maybe my fault... Best, BR -- This e-mail and any attachments do not contain confidential, copyright and or privileged material. Everyone can read it and do with it whatsoever. If you are not the intended addressee or an authorised recipient of the addressee please do not waste any time notifying us of receipt by returning the e-mail because we do not care if you use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of the rest of the world (ROW). ROW Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. ROW Limited (company no. 42) is registered in the Universe with its registered office pretty much anywhere on the 3rd planet including but not limited to Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. -Original Message- From: Marcin Wojdyr [mailto:marcin.woj...@diamond.ac.uk] Sent: Wednesday, January 07, 2015 10:07 AM To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Release 6.5 On Mon, Dec 22, 2014 at 10:43:27AM +0100, Bernhard Rupp wrote: Upon windows upgrade with default settings, the previous desktop icon 6.4 command line C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl will not work anymore. I forgot to reply to this in December. I couldn't reproduce it. The icon was apparently updated (C:\CCP4\6.5\...) by the installer. The command is the same as in the previous versions, except for the path (6.5 instead of 6.4). Hard to tell what didn't work without more details. Sometimes changing environment variables in the registry has no effect until rebooting or logging out and in. Maybe this was the case. Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ccp4i.fat Description: Binary data
[ccp4bb]
Also MATTPROB indicates 3 or 4 molecules/asu as likely solutions. http://tinyurl.com/pe2choc I do not understand why you propose 16 mol/asu? The entire unit cell would likely be only 8 molecules (2 tetramers) BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Remy Loris Sent: Sunday, August 17, 2014 4:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] A back of the envellope calculation shows that your asymmetric unit contains most likely 4 molecules with Vm = 2.16 A3/Da, corresponding to 43% solvent. Searching for 16 molecules is thus nonsense. Remy Loris Vrije Universiteit Brussel On 17/08/14 08:54, Avisek Mondal wrote: Hello everyone, i am struggling with a problem.. My crystal was diffracted at 1.9A in P21 spacegoup with unit cell parameter a=87.7 b=93.9, c=111.78 ,beta=94.98 which contains 16 molecules per assymmetric unit (Molecular weight of the Protein+DNA =56 KDa. actually it is a complex of 40Kda tetramer and 23bpDNA ) .In solution, it shows tetrameric in nature The crystal structure of its homologous structure has been reported earlier (50%identical in amino acid seq.) and it was also a tetramer and its unit cell (also P21) was approximately 4 times less than mine. It showed 4 molecules per assymmetric unit. I didn't get any molecular replacement. All the programms are takings very long time to do it. Although the single crystal is untwinned i think it is a case of pseudosymmetry. Please help me if you have any good suggestion regarding molecular replacement other than experimental phasing.
Re: [ccp4bb] Observations-to-parameter ratio in Refmac
Ethan is right. I also have compiled a few estimates how to get to this number pp638 ff 'Estimating the restraint count' in BMC Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan A Merritt Sent: Tuesday, June 03, 2014 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Observations-to-parameter ratio in Refmac On Tuesday, 03 June, 2014 17:02:56 Klaus F tterer wrote: Does someone know whether Refmac outputs the observations-to-parameters ratio or, failing that, the number of refined parameters in the log file? Klaus This turns out to be much more complex than you might think. See: To B or not to B: a question of resolution? Acta Cryst. D68, 468-477. http://scripts.iucr.org/cgi-bin/paper?S0907444911028320 -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] BMC second edition - request for comments
Dear Fellows and faithful readers of BMC: Many thanks again to the members of the community who have contributed so generously to BMC either with original ideas and comments during its 60 month gestation period or by careful reading and correcting many mistakes and outright errors during post-publication review. An errata page of over 500 entries is quite a sign of community involvement (and less so of my attention to detail). There have been quite some exciting and developments and consolidations of opinions in the field in recent years, and after half a decade, an update of the books seems to be justified. Many of you have also used the book in courses, and now is your chance to voice your critique, comments, and wishes for the second edition. You might express this either informally through email to me or in a more structured response to a simple template I have available on my web site. http://www.ruppweb.org/garland/BMC_2nd_Ed_suggestions.docx ANYTHING you wish to express is fair game, from didactic pointers to subject additions, to offers for review of newly suggested chapters; any material you may have that is worthwhile of/for a better or new figure, and of course, still plenty of typos or poor English (copy editors are human, too). From the pool of useful suggestions I will draw a winner receiving a copy of BMC2. Best wishes, BR Bernhard Rupp k.-k. Hofkristallamt Vista, CA 92084 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
[ccp4bb] OT:Website help
Hi Fellows, please allow me this OT posting I would kindly ask to be continued by interested parties off-board. Summary: I am having serious trouble with my web hosting provider. Problem: My ruppweb/hofkristallamt site which has to a degree become a community resource is hosted on a windows NT server running IIS 5. The Apps are relatively complicated FORTRAN cgi apps compiled as .exe files which need read/execute access to /cgi and write/read access to a scratch directory /write. The hosting service wishes to discontinue this server by Nov 01 as they transition to a linux server. The IIS 5.0 service already crashes daily. To call this a pain in the rear (I never ran a linux web service which I would need for development and transition) is a crude understatement. Possible options: (a) Host the content under linux, and just have the cgi's redirected via http link to an IIS 5.0 server (which nobody has anymore - or does someone?). (b) as above, but to IIS 7.5 . Alas, I cannot get the scripts running under IIS 7.5, but maybe we have an expert around ? (c) If the scripts can be made run under IIS7.5 (it seems to be a server configuration problem, afaik) find a host that uses IIS7.5 or a kind soul that lets me execute the scripts there (any kind masochists running IIS7.5 around)? (d) redesign the whole web site in a modern fashion and recompile/configure for Linux (e) better ideas. I am willing to shell out a (small) stipend for some student or fellow who is knowledgeable and able to manage a transition/ update/redesign/maintain of my site. Please contact me if you have any solutions/ideas/suggestions/interest. Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - A good plan today is better than a perfect plan tomorrow. -
Re: [ccp4bb] popular piece on X-ray crystallography
However, a reviewer could reject the method on theoretical grounds - the explanation of X-ray diffraction as a multi-photon process is not correct BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Artymiuk Sent: Friday, April 19, 2013 7:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] popular piece on X-ray crystallography Just to clarify, Jeremy was not being serious, but imagining what an awkward / obnoxious grant reviewer might have said in 1913. But your points would be valuable in rebutting such a view Pete On 19 Apr 2013, at 11:28, Navdeep Sidhu wrote: Dear Pet, On the contrary, far as I know, nature seems to require most solids we see around us to be crystalline. And much of the rest is either gaseous or plasma. Hence, by the reasoning proposed, we are led to suspect a different conclusion: that it's studies dealing with the remaining state that have little general applicability as the requirement for objects to force themselves into the disordered arrays of the liquid state is an absurd limitation. (However, I'd support funding it nevertheless.) Best regards, Navdeep --- On Fri, Apr 19, 2013 at 10:14:04AM +0100, Peter Artymiuk wrote: Another of my colleagues, Jeremy Craven, is an NMR spectroscopist and bioinformatician. He is in referee mode at present and comments: From: Jeremy Craven c.j.cra...@sheffield.ac.uk Date: 19 April 2013 10:05:18 GMT+01:00 To: Peter Artymiuk p.artym...@sheffield.ac.uk Subject: Re: Fwd: popular piece on X-ray crystallography I suspect this technique will have little general applicability as the requirement for objects to force themselves into ordered arrays is an absurd limitation. I would not support funding it. Jeremy I fear he may be right best wishes Pet On 19 Apr 2013, at 09:53, David Briggs wrote: Following on from that - readers may be interested in Stephen Curry's post in the Guardian, regarding the Crystallography exhibit at the London Science Museum. http://www.guardian.co.uk/science/occams-corner/2013/apr/19/1 regards, Dave David C. Briggs PhD http://about.me/david_briggs On 19 April 2013 09:44, Peter Artymiuk p.artym...@sheffield.ac.uk wrote: Dear all In Britain there is a free newspaper that you can pick up on buses called the Metro. My colleague Geoff Ford pointed out this short feature on the history X-ray crystallography in last Monday's Metro newspaper. I think it's rather good. http://www.cosmonline.co.uk/blog/2013/04/14/conquering-realm-invisi ble best wishes Pete Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND --- Navdeep Sidhu Departments of Structural Chemistry Pediatrics II University of Goettingen Office Address: Institute of Inorganic Chemistry Tammannstrasse 4 37077 Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Phone: +49 551 39 33059 Fax: +49 551 39 22582 Dept. Homepage: http://shelx.uni-ac.gwdg.de/ --- Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
Re: [ccp4bb] popular piece on X-ray crystallography
Simply on grounds that even a single photon can get diffracted (remember the photon counting multiwire detectors?). The phenomenon might be best described as something like a annihilation-creation process a la Feynman. Much of this has been discussed on board before. Mini-summary: 'Multiphoton' somehow invokes at least in my mind necessary inter-photon coherence (to maintain phase relations) between multiple scattered photons, which is in general not the case nor necessary. The Bragg equation pictures showing 2 incoming x-rays are very deceiving. They should be seen as a help to understand the phase relation for the electric field vector of the ONE incoming photon resonating multiple atoms' electrons. The new photon then emerges based on a probability function proportional to the structure factors. You just can't predict which one it will be. That 3d (squared) probability distribution - after you have collected many photons - is your diffraction pattern. Chapter 6 introduction... Best, BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, April 19, 2013 9:44 AM To: b...@hofkristallamt.org Cc: Bernhard Rupp (Hofkristallrat a.D.); CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] popular piece on X-ray crystallography -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Bernhard, could you explain this? A photon is the exchange particle of the electromagnetic force, i.e. as soon as you have more than two charged particles interacting there is more than one photon - why is it incorrect to use the term multi-photon process in the context of X-ray diffraction? Cheers, Tim On 04/19/2013 06:19 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: However, a reviewer could reject the method on theoretical grounds - the explanation of X-ray diffraction as a multi-photon process is not correct BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Artymiuk Sent: Friday, April 19, 2013 7:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] popular piece on X-ray crystallography Just to clarify, Jeremy was not being serious, but imagining what an awkward / obnoxious grant reviewer might have said in 1913. But your points would be valuable in rebutting such a view Pete On 19 Apr 2013, at 11:28, Navdeep Sidhu wrote: Dear Pet, On the contrary, far as I know, nature seems to require most solids we see around us to be crystalline. And much of the rest is either gaseous or plasma. Hence, by the reasoning proposed, we are led to suspect a different conclusion: that it's studies dealing with the remaining state that have little general applicability as the requirement for objects to force themselves into the disordered arrays of the liquid state is an absurd limitation. (However, I'd support funding it nevertheless.) Best regards, Navdeep --- On Fri, Apr 19, 2013 at 10:14:04AM +0100, Peter Artymiuk wrote: Another of my colleagues, Jeremy Craven, is an NMR spectroscopist and bioinformatician. He is in referee mode at present and comments: From: Jeremy Craven c.j.cra...@sheffield.ac.uk Date: 19 April 2013 10:05:18 GMT+01:00 To: Peter Artymiuk p.artym...@sheffield.ac.uk Subject: Re: Fwd: popular piece on X-ray crystallography I suspect this technique will have little general applicability as the requirement for objects to force themselves into ordered arrays is an absurd limitation. I would not support funding it. Jeremy I fear he may be right best wishes Pet On 19 Apr 2013, at 09:53, David Briggs wrote: Following on from that - readers may be interested in Stephen Curry's post in the Guardian, regarding the Crystallography exhibit at the London Science Museum. http://www.guardian.co.uk/science/occams-corner/2013/apr/19/1 regards, Dave David C. Briggs PhD http://about.me/david_briggs On 19 April 2013 09:44, Peter Artymiuk p.artym...@sheffield.ac.uk wrote: Dear all In Britain there is a free newspaper that you can pick up on buses called the Metro. My colleague Geoff Ford pointed out this short feature on the history X-ray crystallography in last Monday's Metro newspaper. I think it's rather good. http://www.cosmonline.co.uk/blog/2013/04/14/conquering-realm-invis i ble best wishes Pete Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND --- Navdeep Sidhu Departments of Structural Chemistry Pediatrics II University of Goettingen Office Address: Institute of Inorganic Chemistry Tammannstrasse 4 37077 Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Phone: +49 551 39 33059 Fax: +49 551 39 22582 Dept. Homepage: http://shelx.uni-ac.gwdg.de/ --- Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University
[ccp4bb] Thx...
Hi Fellows from the programming department(s), I just had the pleasure to work with the new update mechanism and Win CCP4 6.3 GUI. That you can get from the summary page directly to Coot (which also automatically updates) and that everything works as advertised is very impressive and I perhaps even necessary for CCP4 to keep its market share with the push-button crowd. I think it is awesome progress and thanks to all the friendly coders for their efforts. The collective time savings are enormous. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers ---
Re: [ccp4bb] 3D alignment of points (atoms)
A brief description of the Kearsley implementation including F77 code is in the old (1993) computing tutorial: http://www.ruppweb.org/xray/comp/superpos.htm The example program only works with pairwise correspondence but still one gets the idea. Best wishes for 2013, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of George Sheldrick Sent: Thursday, December 27, 2012 1:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D alignment of points (atoms) A computationally elegant and probably faster approach is to use quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent description of this method see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/ George
Re: [ccp4bb] vitrification vs freezing
Agreed. When we do not know what is actually happening upon cooling in a multi-component system like the crystal, avoiding well -defined terms referring to the state of matter, and instead restricting ourselves to a term describing the process appears less contentious. Thus, flash-cooling, cryo-cooling, cryo-quenching all seem permissible to me as they do not refer to the actual and unknown state of matter. Best regards, BR - Knowledge: When you know a thing, to know that you know it, and when you do not know a thing, to recognize that you do not know it. Conficius. -- -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard Bricogne Sent: Friday, November 16, 2012 3:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] vitrification vs freezing Dear all, I think we are perhaps being a little bit insular, or blinkered, in this discussion. The breakthrough we are talking about, and don't know how to call, first occurred not in crystallography but in electron microscopy, in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see for instance http://www.unil.ch/dee/page53292.html). It made possible the direct imaging of molecules in vitrified or vitreous ice and to achieve higher resolution than the previous technique of negative staining. In that context it is obvious that the vitreous state refers to water, not to the macromolecular species embedded in it: the risk of a potential oxymoron in the crystallographic case arises from trying to choose a single adjective to qualify a two-component sample in which those components behave differently under sudden cooling. I have always found that an expression like flash-frozen has a lot going for it: it means that the sample was cooled very quickly, so it describes a process rather than a final state. The fact that this final state preserves the crystalline arrangement of the macromolecule(s), but causes the solvent to go into a vitreous phase, is just part of what every competent reviewer of a crystallographic paper should know, and that ought to avoid the kind of arguments that started this thread. With best wishes, Gerard. -- On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: Hi Sebastiano, I think the term vitrified crystal could be understood as a very nice oxymoron (http://www.oxymoronlist.com/), but it is essentially self-contradictory and not technically correct. As Ethan said, vitrify means turn into glass. Now, a glass state is a disordered solid state by definition, then it can't be a crystal. A vitrified crystal would be a crystal which has lost all three-dimensional ordering, pretty much like the material one gets when using the wrong cryo-protectant. What one usually does is to soak the crystal in a cryo-protectant and then flash-freeze the resulting material, hoping that the crystal structure will be preserved, while the rest remains disordered in a solid state (vitrified), so that it won't produce a diffraction pattern by itself, and will hold the crystal in a fixed position (very convenient for data collection). Moreover, I would say that clarifying a material is vitrified when subjected to liquid N2 temperatures would be required only if you were working with some liquid solvent which might remain in the liquid phase at that temperature, instead of the usual solid disordered state, but this is never the case with protein crystals. So, I vote for frozen crystal.- Javier PS: that comment by James Stroud I forgot to mention that if any dictionary is an authority on the very cold, it would be the Penguin dictionary., is hilarious, we need a Like button in the CCP4bb list! -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-43, Building 1, Room 172-G Mailstop M888 Phone: (505) 667-9376 On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman cbing...@biochem.wisc.eduwrote: cryopreserved It says that the crystals were transferred to cryogenic temperatures in an attempt to increase their lifetime in the beam, and avoids all of the other problems with all of the other language described. I was really trying to stay out of this, because I understand what everyone means with all of their other word choices. On Nov 15, 2012, at 2:07 PM, James Stroud wrote: Isn't cryo-cooled redundant? James On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: Perhaps it's an artisan organic locavore fruit cake. Either way, your *crystal* is not vitrified. The solvent in your crystal might be glassy but your protein better still hold crystalline order (cf. ice) or you've wasted your time. Ergo, cryo-cooled is the description to use. Phil
Re: [ccp4bb] usefulness of cacodylate?
Math may be frightening but cacodylate seems not... With a MW of 214 for the trihydrate a 70 kg clone needs at the 0.5 g/kg LD50 to consume about 35 g of it, which is 0.16M. Of a 0.1M solution you'd therefore have to drink 1.6 L or almost 4 pints. So, prost, cheers, gsuffa, bescheid, slantje, na strovje etc! BR PS: it is really not 0.5mg/g for the LD50 - it is indeed 0.25 to 0.5 g/L - I checked. For waterflea it is lower though... PPS: I remember with horror from my inorganic Chemistry Lab taking place in Boltzmann's Labs (and with the same curriculum as I suspect now), a smell test (as in sniffing into the test tube) for As, called the Cacodylprobe (aka Krokodilprobe). As I am still around (although the As sniffing may explain a few things) panic appears unwarranted. - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ --- The road to scientific serfdom is paved with Nature papers --- -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Friday, November 09, 2012 4:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] usefulness of cacodylate? Hi all - Anybody know a) how hazardous is cacodylate? b) does it really matter for crystallization screens? It seems by far the most hazardous component of the standard screens; this 2011 paper seems to think so (bizarrely, I can't access it from Oxford): http://onlinelibrary.wiley.com/doi/10./j.1365-2818.1977.tb01136.x/abstra ct and this is site says lethal dose is 0.5-5g/kg: http://cameochemicals.noaa.gov/chemical/4468 meaning 2ml of a 0.1M solution contains 1/10th lethal dose...? (Someone should check my maths...) [Coarse screens come mixed 2ml per condition.] Has anybody done careful experiments that showed it really mattered for a given crystal -- or even an entire screen? So I'm inclined to toss it out entirely rather than make crystallization screening a hazardous activity. (We're being subjected to a safety review.) Thoughts welcome. phx
Re: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure
An example for how crystallization at non-physiological pH (and non-physiological concentrations and non-physiological environmental) may influence behavior of the protein is the Botulinum A LC protease. Under normal conditions (upon endocytosis of a few molecules at best into the nerve cell), it works like a canonical serine protease, but at pH 4.6 it cleaves itself in a non-canonical fashion, i.e. with a loop resembling the target peptide running opposite direction. Later isoform structures solved at neutral pH showed normal, canonical protease activity. http://www.ruppweb.org/cvs/br/Segelke_2004_PNAS_botulinum_neurotoxin.pdf BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Acoot Brett Sent: Saturday, October 27, 2012 8:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot
Re: [ccp4bb] PNAS on fraud
I think the real point here is that a difference exits between divergent interpretation of legitimate evidence - which is normal scientific epistemology - or whether the presented 'evidence' is in some fashion tampered with. The former is healthy procedure and (I hope) not subject of disagreement - we all have been wrong a few times at least and corrected either by better insight or new evidence (or actually useful reviews) - and the question boils down to where 'tampering' with evidence starts. Is willful neglect of contrary results tinkering? Is looking only for reinforcing data already tinkering (aka expectation and confirmation bias)? It is easy to judge in the case of poorly fabricated stuff like bet V1 or c3b, but I think the borderline cases are potentially much more damaging. Btw, I have few more references to the psychology of science Koehler JJ (1993) The Influence of Prior Beliefs on Scientific Judgments of Evidence Quality. Organizational Behavior and Human Decision Processes 56(1): 28-55. Simmons JP, Nelson LD and Simonsohn U (2011) False-Positive Psychology: Undisclosed Flexibility in Data Collection and Analysis Allows Presenting Anything as Significant. Psychological Science: DOI: 10.1177/0956797611417632. Frey BS (2003) Publishing as Prostitution? Choosing Between Ones Own Ideas and Academic Failure. Public Choice 116, 205-223 (ETHZ) Nice weekend reading. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of George DeTitta Sent: Friday, October 19, 2012 10:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This gets us more into the philosophy of science but I've always felt authors had a right to speculate in the discussion sections of their papers on what it all means. And speculate even past the information in the actual data (see for example the wonderfully prescient final lines of the Watson Crick paper). As long as the experiments are fully described and the confidence of the data is clearly spelled out. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8611 (voice) (716) 480-8615 (mobile) (716) 898-8660 (fax) deti...@hwi.buffalo.edu www.hwi.buffalo.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Friday, October 19, 2012 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re: [ccp4bb] PNAS on fraud Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and
[ccp4bb] PNAS on fraud
Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] PNAS on fraud
One might include independent prior evidence (Kleywegt, Brown @ Ramaswami) showing that in general most other quality indicators are worse for high impact journals. So, as a frequentist I agree that his correlation is significantly weak, as a Bayesian I say it is reasonably probable. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
Re: [ccp4bb] PNAS on fraud
Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
Re: [ccp4bb] Question about weird diffraction map
Hmmm..I just fail to see 'lines' in that diffraction map. I see spots along something that could be segments of diffraction rings, i.e. a number of these crystals in some clustered random orientations, similar to ice as you mention. I also wonder how there could be true diffraction 'lines': If it is a small molecule or salt, then the diffraction spots are pretty far apart in reciprocal space, and the chance of seeing diffraction lines of closely spaced adjacent RL points like we see in the lunes of a (single X) macromolecular rotation image is quite remote. If for example that spot cluster down left would be a 'line', then the lattice spacing would have to be quite large. Why some of the low resolution rings are not exactly rings either can have various reasons we can discuss off board. Otherwise no dissent. Best, BR From: Matthew Franklin [mailto:mfrank...@nysbc.org] Sent: Tuesday, July 24, 2012 7:08 AM To: b...@hofkristallamt.org Cc: Bernhard Rupp (Hofkristallrat a.D.); CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Question about weird diffraction map Hi Bernhard - Having the spots in regular lines indicates that this is a single crystal diffraction pattern (to a first approximation). I have seen ice rings which contain a few strong spots, probably from microcrystals of ice, but I haven't yet seen ice diffraction that shows a lattice of spots. So, the presence of the spot lattice, plus the spots below 3.9 A, allow one to say that this image isn't ice diffraction on top of weak/absent protein diffraction. Ergo, this crystal is not a macromolecule. Plus, I was trying to show Zhao that the spots aren't just scattered at random. - Matt On 7/23/12 5:25 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: you'll see that some of them are arranged in regular lines. I am not sure I understand what the line argument implies? indicates a very small unit cell, with dimensions probably 10 A Very indicative also the few strong and isolated high resolution reflections Cheers, BR -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] linking PLP-Lys
Link statement? LINK NZ LYS A 72 C4A PLP A 500 1555 1555 1.30 There are many examples in the PDB this one 1hkv Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh Kumar Sent: Monday, July 23, 2012 10:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] linking PLP-Lys Dear All, My friend needs a help. What is the best way to connect Lys to PLP with covalent bond. I am sure there are many ways do it. My friend would appreciate if you could simplify and explain this so that he could learn it without difficulties. Also I could learn I appreciate your time and help Thanks Rajesh
Re: [ccp4bb] Question about weird diffraction map
you'll see that some of them are arranged in regular lines. I am not sure I understand what the line argument implies? indicates a very small unit cell, with dimensions probably 10 A Very indicative also the few strong and isolated high resolution reflections Cheers, BR
Re: [ccp4bb] Crystal Optimization
Always give up. ...definitely not the kind of guy I want to sit up front in an airliner… Best regards, BR - Bernhard Rupp, ATP-B737, CFII-MEI Vienna Air International Professional Aviation Services 001 (925) 209-7429 +43 (676) 571-0536 b...@vienna-air.com b...@ruppweb.org http://www.vienna-air.com/ - It is not your aptitude but your attitude that determines your altitude. (or your crystals) - From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of yybbll Sent: Tuesday, July 10, 2012 11:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal Optimization Hi, In my experience, it is very very very difficult to optimize this needle like crystal. Always give up. Good luck! Dear All; Could somebody give a nice suggestion how the following type crystal could be optimized, I almost tried everything. Crystal Image is attached Crystal condition: 20% w/v PEG3350 and 200mM NaCl. Thanks in advance Bashir -- Muhammad Bashir Khan ** Structural Genome Consortium (SGC). University of Toronto Toronto, Canada
Re: [ccp4bb] information received through the AFC: iycr2014
Ø enjoy that the U.N.'s declaration of the International Year of Crystallography comes in the form of a resolution. ...which tells what a UN resolution is worth BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sampson, Jared Sent: Thursday, July 05, 2012 10:23 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] information received through the AFC: iycr2014 I particularly enjoy that the U.N.'s declaration of the International Year of Crystallography comes in the form of a resolution. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 4, 2012, at 8:03 AM, Vellieux Frederic wrote:
[ccp4bb] [OT]: The Ultimate Inferior Beings
This is to inform you that a well-respected member of the crystallographic community has published a totally hilariously absurdly funny Sci-Fi novel. I added a link on my web site, www.ruppweb.org , and no, I said 'well respected', so I did not write it, but maybe you can guess from the pseudonym. Cheers, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] The effect of His-tag location on crystallization
Google yields amongst others: His-tag impact on structure Acta Cryst. (2007). D63, 295301 ...quäl dich. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of weliu Sent: Tuesday, June 26, 2012 6:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] The effect of His-tag location on crystallization Dear all, We crystallized a protein and found that crystal quality greatly depended on the location of His-tag. When a His-tag was added at the C-terminus, only crystalline precipitate or spherical quasi crystals were grown. However, when the His-tag was moved to the N-terminus, single crystals were grown under a number of conditions, and the best one diffracted to 1.7 angstrom after optimization. I was wondering if there were published reports describing similar cases. Thank you in advance Wei Liu
[ccp4bb] FW: [PyMOL] Structural biologist job
FYI for the on-pymol readers. BR -Original Message- From: H. Adam Steinberg [mailto:a...@steinbergs.us] Sent: Tuesday, June 12, 2012 4:22 AM To: pymol-us...@lists.sourceforge.net Subject: [PyMOL] Structural biologist job Hi all, A friend of mine is looking to hire a structural biologist. With the tight job market I though I would try and get this out to as many people as possible. I am looking to hire a PhD structural biologist to join the team I manage at Myriad Genetic Laboratories in Salt Lake City, Utah. Please forward/post/pin-up the attached pdf if you can think of anybody who might be interested, or if you can think of someone that might know someone who might be interested. Myriad Genetics is a great company to work for, with all the perks of a biotech company (employee stock option purchase plan, 401k company match, full benefits, etc). Myriad Genetics is nestled in the foothills of the Rocky Mountains with over 1,100 employees and growing. Salt Lake City is a great place to live both for the outdoorsy person, as well as the cultural arts type person. It s also a great place to raise a family. Please email all job inquiries to Dr. Julie Eggington at jeggi...@myriad.com. Thank you. Julie Myriad Genetics - Clinical Variant Specialist unofficial job posting 2012.pdf JOB OPENING: Clinical Variant Specialist Requires Ph.D. in Biochemistry or related field, with emphasis in structural biology. Location: Myriad Genetic Laboratories, Inc. Salt Lake City, UT. Full time position NOTE: This is an early, unofficial job posting. Official job postings are found at www.myriad.com Overview: Myriad Genetic Laboratories is a leading molecular diagnostic company based in Salt Lake City, Utah. Myriad offers predictive medicine tests that identify hereditary breast and ovarian cancer, hereditary colorectal and uterine cancer, and other hereditary cancer syndromes. DNA sequencing allows Myriad to detect these syndromes by identifying disease causing mutations in specific genes. However, not all genetic variants which are identified in DNA testing are disease causing. Initially, some variants are classified as Genetic Variant of Uncertain Significance until research shows whether or not the genetic variant is disease causing or benign. It is the role of Myriad's Variant Specialist Team to collect and analyze data so that these Genetic Variants of Uncertain Significance can be correctly classified in a clinical setting. The Variant Specialist Team is looking to hire an expert in structural biology. Unlike traditional Scientist I/II positions in biotechnology, the Clinical Variant Specialist is not likely to pursue lab bench work, but will apply his/her skills to reviewing literature and using molecular modeling and bio-informatics approaches to assist in better understanding the effects of genetic mutations. The Clinical Variant Specialist will work within a larger group of cross-disciplinary scientists and statisticians. Additionally, the Clinical Variant Specialist will work with clinician customers to assist in scientific understanding and in the coordination of research studies. Excellent communication skills are required. Attendance at professional meetings and publication opportunities are fostered. The clinical Variant Specialist will also work on a variety of projects across different non-science divisions within Myriad as a representative of the Variant Specialist Team. Qualifications: -Ph.D. in Biochemistry or a related field required, with emphasis in structural biology -Excellent written and verbal communication skills -Candidates with postdoctoral research experience or equivalent are preferred -Candidates with experience in protein-nucleic acid interactions and/or experience in cancer causing biological pathways are preferred How to apply: -Applications are to be formally made through http://www.myriad.com/careers/ when the position officially posts (likely in July 2012). The position may have a different title at time of posting. Dr. Julie Eggington is seeking resumes early to screen candidates as soon as possible starting in June 2012. To facilitate this, please email resumes and enquiries to Dr. Julie Eggington at jeggi...@myriad.com with Clinical Variant Specialist Job Opening in the subject line. About Myriad: Myriad Genetics, Inc. (Nasdaq: MYGN) is a leading molecular diagnostic company dedicated to making a difference in patient s lives through the discovery and commercialization of transformative tests to assess a person s risk of developing disease, guide treatment decisions and assess risk of disease progression and recurrence. With fiscal year 2011 revenue of over $400 million and more than 1,100 employees, Myriad is working on strategic directives, including new test introductions, companion diagnostics, and international expansion, to take advantage of significant
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Richard Dickerson's book is relevant and gripping reading http://www.amazon.com/gp/product/0878931686?ie=UTF8tag=brscrystallot-20lin kCode=as2camp=1789creative=9325creativeASIN=0878931686 BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of aaleshin Sent: Wednesday, June 06, 2012 11:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? I wonder if anyone attempted to write a historic book on development of crystallography. That generation of crystallographers is leaving this world and soon nobody will be able to say how the protein and non-protein structures were solved in those days. Alex
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely different that the local neighbor environment/geometry which can be backtransformed - although with quite some uncertainty - from the EXAFS wiggles). Any argument about absolute f peak values in absence of experimental evidence (scan) might want to consider that. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * 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 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Given Cu, yes, the five M edges between 2.3keV and 3.6keV contribute a continuum transition signal of the 8e- you initially referred to. -Original Message- From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: Wednesday, June 06, 2012 12:35 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? But the edges for I and Hg are pretty far from CuKa (see attached). I am familiar with their being extra signal (white lines) very close to the peak, but not so far away JPK
Re: [ccp4bb] to determine missing atoms and residues in a PDB file
I do not seem to understand the meaning of fixing. Fixing something can mean a) repairing it, implying that something was broken or amiss. Lack of experimental information expressed as omission of atoms is not something that needs fixing. b) keeping it constant. Like in having one single energy minimized conformation and accepting it once fixed as in (a). c) injection of conscience-expanding drugs, often also hallucinogenic, as in fixing in (b). d) removal of reproductive organs, as in possible punishment for mutilating experimental structure models by fixing as in (a,b,c) A discrete ensemble of probable rotamers following a distribution with constrained occupancy probabilities according to their empirically observed frequency (optimally context sensitive) might be an approximate solution to a to this date quite contentious issue. I am sure Paul will make it happen ;-) Anyhow - beware of fixers. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of debayan dey Sent: Wednesday, May 30, 2012 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] to determine missing atoms and residues in a PDB file The missing residues/atoms in the PDB file can be found out and fixed in Schrödinger program's Prime module refinement.It will automatically detect the missing atoms in a residue and will fix it. After fixing it can energy minimize it.For missing portions of residue it can build the missing portions using homology model.The other option for fixing missing atoms is to use the following server: http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php -Debayan Dey On Wed, May 30, 2012 at 5:20 PM, sreetama das somon_...@yahoo.co.in wrote: Dear All, I have a PDB file which does not have the REMARKS cards 465 (for missing residues) and 470 (for missing atoms). This is not a deposited PDB file. Is there any program to figure out the missing residues and atoms (some programs complain about missing atoms) ? Or do I have to check in any particular file generated during the processing of the diffraction data? The S2C program from Prof. Dunbrack's Lab does not show any option of uploading pdb files (this solution was mentioned to a previous query on the BB). Thanks in advance, sreetama -- Debayan Dey Research Fellow Dept. of Physics, Biocrystallography and Computational Biology Laboratory Indian Institute of Science India
Re: [ccp4bb] Covert Structure Factor to mtz
It would be desirable to actually HAVE the cell information in the cif file, if simply for assuring/checking consistency between model and data. Maybe something for the PDB to contemplate BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of martyn.w...@stfc.ac.uk Sent: Thursday, May 17, 2012 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Covert Structure Factor to mtz Reflection cif files from the PDB do not always have cell and symmetry information in them, particularly the older ones, and it sounds like this is your case. In that case, you need to manually copy the cell information from the PDB web page into the ccp4i interface before running. HTH Martyn
[ccp4bb] [OT] to CCP admin - CCP14 - who's in charge?
Dear CCPx administrators: I just notice that on /www.ccp14.ac.uk/ccp/web-mirrors/llnlrupp/cvs/Rupp/rupp.html a deprecated web page from the early 2000s (!) that causes confusion exists on a mirror of the LLNL site dead since 2005. I cannot find a responsible contact for CCP14 since Lachlan's unfortunate demise. The last person in charge of the CCP14 website was William Bisson, but the contact link in the page goes to an uninformative site. Who might be in charge there or a responsive contact? Best regards, BR
Re: [ccp4bb] very informative - Trends in Data Fabrication
You never know when a forgotten slip of the mouse when using AutoDep ten years ago will come back to haunt you. On the paper James refers to and found the data, added mystery was that the postdoc who may have slipped disappeared w/o much of trace and the PI died. Dan was the only survivor. Still they found the data. BR
[ccp4bb] Refmac executables - win vs linux in RHEL VM
Something the developers might be interested in: The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x slower than those from the linux distribution run **in a RHEL6.2-64 VMware virtual machine hosted the same windows7/64 system.** VM/RHEL: Refmac_5.6.0117: End of Refmac_5.6.0117 Times: User:1015.3s System: 135.0s Elapsed:19:17 Win native Refmac_5.6.0117: End of Refmac_5.6.0117 Times: User: 0.0s System:0.0s Elapsed:67:49 Most peculiaralthough I think but I do not know whether the linux binaries are 64 bit I don't think that address space is the issue here if they are. Maybe the paranoia-checkers in windows slow everything down although I did not see any resources overwhelmed... Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] very informative - Trends in Data Fabrication
I also don't really worry about the images as a primary means of fraud prevention, although such may be a useful side effect. These cases are spectacular but so rare that it indeed would not primarily justify the effort. That it can be a useful political instrument to make that argument and get funding, may be, but that is a bit of a double edged sword and harm can be done see (5) The real point to me seems - a) is there something in the images and in between casually indexed main reflections we do not use right now that allows us to ultimately get better structures? I think there is, and it has been told before, from superstructures, modulation, diffuse contributions etc etc. A processed data file does not help here. But do we need the old image data for that or rather use new ones from modern detectors? Where is the cost/benefit cutoff here? b) looking at how some structures are refined, there is little reason to believe that data processing would be done more competently by untrained casual users (except that much of the data processing is done with the help of beam line personnel who rather know how to do it). Had we images, the next step then could be PDB_reprocess. A processed data file does not help much there either. c) Discarding your primary data is generally considered bad form... @AlexA: Arguing with the PDB is not really useful. They did not generate the bad data. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald E Stenkamp Sent: Thursday, April 05, 2012 1:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication This discussion has been interesting, and it's provided an interesting forum for those interested in dealing with fraud in science. I've not contributed anything to this thread, but the message from Alexander Aleshin prodded me to say some things that I haven't heard expressed before. 1. The sky is not falling! The errors in the birch pollen antigen pointed out by Bernhard are interesting, and the reasons behind them might be troubling. However, the self-correcting functions of scientific research found the errors, and current publication methods permitted an airing of the problem. It took some effort, but the scientific method prevailed. 2. Depositing raw data frames will make little difference in identifying and correcting structural problems like this one. Nor will new requirements for deposition of this or that detail. What's needed for finding the problems is time and interest on the part of someone who's able to look at a structure critically. Deposition of additional information could be important for that critical look, but deposition alone (at least with today's software) will not be sufficient to find incorrect structures. 3. The responsibility for a fraudulent or wrong or poorly-determined structure lies with the investigator, not the society of crystallographers. My political leanings are left-of-central, but I still believe in individual responsibility for behavior and actions. If someone messes up a structure, they're accountable for the results. 4. Adding to the deposition requirements will not make our science more efficient. Perhaps it's different in other countries, but the administrative burden for doing research in the United States is growing. It would be interesting to know the balance between the waste that comes from a wrong structure and the waste that comes from having each of us deal with additional deposition requirements. 5. The real danger that arises from cases of wrong or fraudulent science is that it erodes the trust we have in each others results. No one has time or resources to check everything, so science is based on trust. There are efforts underway outside crystallographic circles to address this larger threat to all science, and we should be participating in those discussions as much as possible. Ron On Thu, 5 Apr 2012, aaleshin wrote: Dear John,Thank you for a very informative letter about the IUCr activities towards archiving the experimental data. I feel that I did not explain myself properly. I do not object archiving the raw data, I just believe that current methodology of validating data at PDB is insufficiently robust and requires a modification. Implementation of the raw image storage and validation will take a considerable time, while the recent incidents of a presumable data frauds demonstrate that the issue is urgent. Moreover, presenting the calculated structural factors in place of the experimental data is not the only abuse that the current validation procedure encourages to do. There might be more numerous occurances of data massaging like overestimation of the resolution or data quality, the system does not allow to verify them. IUCr and PDB follows the American taxation policy, where the responsibility for a fraud is placed on people, and the agency
Re: [ccp4bb] very informative - Trends in Data Fabrication
Ojweh c) Discarding your primary data is generally considered bad form... Agreed, but it is a big burden on labs to maintain archives of their raw data indefinitely. Even IRS allows to discard them after some time. But you DO have to file in the first place, right? How long to keep is an entirely different question. What is wrong with partially integrated data in terms of structure validation? Who thinks something is wrong with that idea? Section 3.1 under figure 3 of said incendiary pamphlet states: '...yadayadawhen unmerged data or images for proper reprocessing are not available owing to the unfortunate absence of a formal obligation to deposit unmerged intensity data or diffraction images.' They did not generate the bad data. This is a genuine American thinking! Ok, the US citizens on BB might take this one up on my behalf, gospodin ;-) видеть вас на Лубянке. But they might create conditions that would prevent their deposition. Sure. We are back to the 2007 Reid shoe bomber argument. If you make PDB deposition a total pain for everybody, you don't get compliance, you get defiance. Ever seen any happy faces in a TSA check line? Anyhow, image deposition will come. Over and out, BR
[ccp4bb] arp_waters still available?
Dear Developers, in some older scripts I still call the ccp4 version of arp_waters, which worked well for dummy atom picking. It does not seem to be included in recent 64 bit CCP4 packages. Does anyone perhaps have a precompiled 64 bit version of arp_waters that might run on RHEL62? Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] Who is using 64-bit Linux?
I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i, coot, and shelxcde beta executables run fine. There were issues with the coot package installation due to unresolved dependencies and my ignorance thereof, but I think a working RHEL62-64 compatible package is available now, the coot wiki has latest info. I could not get Xtalview running, probably some xterm thing beyond my grasp, which also screws up the latest hkl2mapV0.3, V0.2 runs fine. Free intel ifort runs great. The great part about the VM ware installation is that I also got it running on a win7-64 8GB laptop by simply copying the virtual RHEL machine (files). That alone saved a few day's work. Also the Unity feature of VMware is a blast. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Tuesday, April 03, 2012 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] very informative - Trends in Data Fabrication
Orcus, if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. The skill of presentation is at least as important in Science as being right. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin
Re: [ccp4bb] very uninformative
Ok Kevin, thank you for your response. You got it, and that is good, and I am sure we'll hear from you again and that is good too. But let me explain the Orcus (however, keep in mind, I am only a single contributor and almost always do not represent the majority of CCP4BB users' opinions. So that alone should be some comfort). The title of Orcus means that you have earned yourself a nickname. Nicknames are a brutal invention, common in Western civilization, almost always addressing some personal idiosyncrasy, in general politically incorrect, but nevertheless they stick*). So let me explain: St. Orcus is the patron saint of trolls, hobgoblins and troglodytes, and the defender of off-topic posters and otherwise chastised contributors (just like the Hofkristallrat sitting in his Hofkristallamt is the defender of structures collected from real data. That is for example why I do not get invited to modelers' conferences. Everything has its price). So you are now in the unique position to evaluate the orcness of a contribution - perhaps first by making sure that your own contributions are not orcish - and exercise your right to identify any contributions you consider orcward. Experiencing a new culture can be a confusing and upsetting experience. If I may offer some comforting example relating to your blogs, and coming from a different planet myself, I once considered it a shocking calamity that protein-ligand structures are published that do not contain a ligand. I have mellowed a lot since and prevented a few cardiac events and assassination attempts by accepting the editorial indifference towards such orcward orcness. Maybe you'll get there too, and maybe you'll become a Hofkristallamtsapprentice. But let me tell you, if you are serious about correcting poor science, you've got to be ready to take a lot more flak to get there than being beatified on the BB. Oh, and by the way, no academic career. Wingardium Leviosa! Over and out, B *) Like Kim Jong-il probably means something like Gold Upright Sun. Just to demonstrate how poor those things translate into reality.. PS: Orcward ligand orcs, the Amt is watching! PPS: it is still ok to ride a trolley. From: Kevin Jin [mailto:kevin...@gmail.com] Sent: Tuesday, April 03, 2012 5:23 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote:
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Guys, http://www.youtube.com/watch?v=CobZuaPMQHw second 9 in this 22 sec video -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Monday, April 02, 2012 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard
Re: [ccp4bb] very informative - Trends in Data Fabrication
Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat außer Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse . Ø And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions on BB and then some, and to all those who actually read BMC and submitted errata. Best regards, BR - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 hofkristall...@gmail.com b...@hofkristallamt.org http://www.ruppweb.org/ -- Once the sun of science is standing low, even dwarfs cast tall shadows --
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
I wish to point out (because I remembered just now) that I offered a similar service after the Murthy scandal on this BB in August 2007: http://www.ruppweb.org/new_comp/frame_maker.html - and JK proposed a value-added contribution. See attached. Btw, Kim Henrick's analysis from 2007 still seems rather lucid to me. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, April 02, 2012 8:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Requested: Three-Day Data Fabrication Workshop Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** ---BeginMessage--- In response to your website, I was thinking of a startup collecting old photos of crystals (harder to computer-generate) to go with the frames--interested in a collaboration? Maybe you could just put a link on your page? JPK ==Original message text=== On Fri, 17 Aug 2007 3:24:45 pm CDT Bernhard Rupp wrote: The PDB is missing a business opportunity. If authors pay 1000s of dollars for publication in high impact journals, they might as well pay a few bucks for image deposition. If I could get my images stored reliably and perpetually for something like $20-50 a pop, I'd do it. Do you know where your favourite frames from 1998 are? Image storage is a good idea *in itself*, but as an enforcement tool it only will make the *exceedingly few* Reids more inventive. PS: Frames for sale. http://www.ruppweb.org/new_comp/frame_maker.html -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Friday, August 17, 2007 7:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Richard Reid and the PDB After Richard Reid more than 100 million people each year have to have their shoes examined and one effect is that older buildings like Heathrow Terminal 3 is the most painful place on earth, the cost of someone trying light their shoelaces has affect us all. The discussion on archiving image data sets - I guess that less than 1% of the image sets for PDB entries are useful to software development (and can be got privately) I guess that maybe 1 in 10,000 entries have a series problem that may require referees to look at the images (and can be accessed upon demand) The cost of disks for your PC - kitchen table disks from a supermarket, may be $1 per Gbyte on USB i/o but an archive centre required to maintain the data will probably need RAID 0/1 - RAID 10, this has high performance, and highest data protection, i.e. can tolerate multiple drive failures, but has high redundancy cost overhead, if you havent noticed a large collection of disks has failures. Look up the problems that the series of Landsat satellites have had from 1980 onwards with the problems arising out of the volume of data and the short life of computer compatible tapes and optical discs. Archiving data lacks glamour its the boring day to day rectification and storage of information, very little money gets spent on this task,for remote sensing the most significant cost is transmission/correction and archiving the data - Three semi-trailer loads of Landsat tapes were found (literally) moldering in a damp basement in Baltimore after people and funding agencies lost interest. Oh yes and detectors change every 5 years and processing software gets lost. At the EBI before we even get a single disk we pay ,000 for a cabinet - disks cost around for 300gigbytes (and not the best disks these are around the same cost for 146 Gigbytes). Disk technology changes every 5 years - an archive cost is to recover the data ever 5 years onto the next generation of hardware. Molecular
Re: [ccp4bb] very informative - Trends in Data Fabrication
orcus impudens From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kendall Nettles Sent: Sunday, April 01, 2012 1:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication What is the single Latin word for troll? Kendall On Apr 1, 2012, at 3:06 PM, Kevin Jin kevin...@gmail.com wrote: “I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate andinterpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map...” You are right! Actually, I am not an experienced protein crystallographer. I have learnt a lot from CCP4BB. I may have paid too much attention to bonding angle and bond length, like in small molecule. This may be an example to share with you. When I worked on those nitroreductase complexed with FMN in 2009 (?), I always observed that the flavin ring presented a strange geometry after refinement. Indeed, I had used the definition of FMN from CCP4 library all the time. In some cases, the methyl group at position of either 7a or 8a was bent off the aromatic ring, if the whole the rest of flavin was restrained in a flat plane. According to my limited knowledge from organic chemistry, carbon of 7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could those methyl groups be bent as sp3 hybridization? Any chemistry behind? With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron density map was a bent along the N5-N10 axis. The bend angle was around ~16 degree. Again, I questioned myself why it was bent? Should this be correct? According to my limited knowledge in chemistry, N10 should be sp3 configuration even if FMN is in its oxidization form, in which the flavin ring should be bent. A quick “google” immediately gave me a link to a very nice paper published by David W. Rodgers in 2002. http://www.jbc.org/content/277/13/11513.full.pdf+html According to this paper, Yes! “In the oxidized enzyme, the flavin ring system adopts a strongly bent (16°) conformation, and the bend increases (25°) in the reduced form of the enzyme,…” When I reported this in the group meeting, I was laughed and told that this is just a model bias. It was over interpreted. Nobody has such sharp vision on electron density map. If this was correct, why nobody could find this and report to CCP4 within last 7 years? Eventually, a senior team member emailed to CCP4 about this issue. Since then, the definition of FMN was updated, according to my suggestion. I was asked “how did you find it?”……. “why you believed you are so right?” I really don’t how to answer. Je pense donc je suis Kevin On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine. But they can't just magic funding and positions into existence... If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated. 1. All of data was correct and real, Hmmm... It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate and interpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map... Paul. -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hi Fellow BBers, I wish to point out that a) this is not an April fools joke, b) but on the other hand it shows (a little buried in the recommendations, and misspelled AFTER proofing) that people who properly do catalogue and preserve images actually can fix deposition errors (compliments to Daniel Minor and James Holton for first finding 2002 images and then reprocessing/depositing the Fobs) c) Due to the unusually high interest in reprints, I probably need to talk to Chester if one of these copies with the cover page authorizing author distribution is available, and then send the links. Best regards, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Saturday, March 31, 2012 8:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] very informative - Trends in Data Fabrication really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen
Re: [ccp4bb] very informative - Trends in Data Fabrication
This is an unresolved problem, and no real satisfactory solution exists, because the underlying reasons for zero occupancy can be different. For people who understand this and look at electron density, it is not a problem. For users who rely on some graphics program displaying only atom coordinates, it can be. The same holds for manipulation of B-factors, trading high B-factors against reduced occupancy, and other (almost always purely cosmetic but still confusing or inconsistent) practices. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nian Huang Sent: Saturday, March 31, 2012 11:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication I don't model zero occupancy in my model. But can't the refinement programs just treat those atoms with zero occupancy as missing atoms? Nian Huang On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421 http://dx.doi.org/10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20 B. B. Rupp Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78 3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78 3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4 1fm4). A variety of analytical tools, including the application of Diederichs plots, R[sigma] plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 tel:%2B1-410-614-4742 Lab: +1-410-614-4894 tel:%2B1-410-614-4894 Fax: +1-410-955-2926 tel:%2B1-410-955-2926 http://web.mac.com/bosch_lab/ image001.gif
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hofkristallrat außer Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse . Ø And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions on BB and then some, and to all those who actually read BMC and submitted errata. Best regards, BR - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 hofkristall...@gmail.com b...@hofkristallamt.org http://www.ruppweb.org/ -- Once the sun of science is standing low, even dwarfs cast tall shadows --
Re: [ccp4bb] very informative - Trends in Data Fabrication
Btw, Table 1 would have fooled me as referee. Not if the bulk solvent parameters would be reported or validated. See recommendations. Best, BR
Re: [ccp4bb] REFMAC5 residues with bad geometry
phenix.refine allows any number of alternate conformers. Hmm. quoting our old friends from the validation circuit: Where freedom is given, liberties will be taken BR
Re: [ccp4bb] Refining Against Reflections?
As you observe, radiation damage is local, but the effect is - to different extent - on all Fs i.e. global (all atoms and their damage contribute to each hkl). So one would need additional local parameters (reducing N/P) if you want to address it as such, your use of occupancy is an example (even if you have a reflection-specific decay, somehow a realistic underlying atomic model would be desirable, and just changing occ might not be ideal)..So is the question then 'Could a reflection-specific time dependent decay factor translate into any useful atom-specific model parameter? BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, March 19, 2012 7:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refining Against Reflections? Dear Crystallographers, it occurred to me that most datasets, at least certainly since the advent of synchrotrons, have probably some degree of radiation damage, if not some huge degree thereof. Therefore, I was thinking an exposure-dependent parameter might be introduced into the atomic models, as an exposure-dependent occupancy of sorts. However, this would require refinement programs to use individual observations as data rather than combined reflections, effectively integrating scaling into refinement. Is there any talk of doing this? I think the hardware could reasonably handle this now? And, besides the question of radiation damage, isn't it perhaps reasonable to integrate scaling into refinement now anyway, since the constraints of hardware are so much lower? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Matthews coeff. from model
I can't imagine the results would be very different for protein-DNA vs. protein-RNA. The reason protein-nucleic acids is an extra category in mattprob is largely due to poorer statistics resulting from limited sample size and hence no reliable resolution dependence can be computed. In addition the partial specific volumes for protein (0.74 cm3/g) and nucleic acids (0.50 cm3/g) are different, so an exact calculation needs to consider their ratio to obtain the correct psv estimate BR - Original Message - From: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, March 12, 2012 11:07:29 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Matthews coeff. from model -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear James, I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base to calculate the solvent content by hand. Regards, Tim On 03/12/2012 06:35 PM, james09 pruza wrote: Dear CCP4bbers, Is there any tool to calculate the Matthews coefficient from a crystallographic model of RNA-protein complex? Thanking you. James. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -END PGP SIGNATURE- -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Water
Ø Some of these 'water' have more than 4 contacts, I would consider them as 'false'. How about bifurcated hydrogen bonds? BR
Re: [ccp4bb] Desalting columns
Why, in the first place, do you feel an urge to concentrate your protein above 3 mg/ml ? For crystallization, the concentration needs to be a) high enough to achieve supersaturation, meaning close enough to the maximum solubility in a given buffer so that the precipitant can drive the system in to supersaturation, preferably of a level where homogenous nucleation can occur (or you micro-seed, if necessary) b) high enough that sufficient material for crystals of acceptable size to grow is in the drop, which is generally the case, lest micro-crystal showers happen. There is ample evidence for proteins crystallizing below 3 mg/ml. The often quoted PDB/BMCD average of somewhere around 10 mg/ml is biased towards highly soluble, smaller (lower hanging fruit) proteins. Sometimes the shape of a distribution matters ;-) BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sangeetha Vedula Sent: Monday, February 27, 2012 8:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Desalting columns Dear bb users, I am trying to crystallize a ~320 kDa protein that crashes out if concentrated past about 3 mg/mL. I would like to try to exchange it into various buffer-salt-additive combinations to see which buffer works. For a starting point, I'd like to use desalting colums. Does anyone have suggestions for good buffer exchange and sample recovery? I woud like to load about 250 uL onto each column. Thanks a lot! Best regards, Sangeetha.
Re: [ccp4bb] Desalting columns
Ø in 2004. Of the 1000 entries that listed [protein], 46 proteins were crystallized below 3.1 mg/ml. That is not necessarily the success rate for low concentrations, which we actually would like to have. We would need negatives for 3 for to give a correct answer. I guess even occurrence might be more frequent now. hintSomething for our center data miners who have the negatives kept /hint. Anecdotally, my personal below-3-occurance brag not success, that is 100% /brag is ~15%, but that does not mean much. Even if it were the success rate: 5% chance compared to zero chance when precipitated Id take it and probably learn something useful during the experiment. BR
Re: [ccp4bb] Aggregated protein for crystallization
You might get lucky by setting up crystallization plates, but chances are you won't get very useful information from them, especially if your aggregated protein is soluble. I seem to fail to understand how crystallization plates would give information in the not-special case of protein aggregates NOT being soluble? BR Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
Re: [ccp4bb] Aggregated protein for crystallization
Well, depends on what 'aggregated' really means. If it implies reasonably weak oligomerization interaction - and it might not be too strong given that the oligomers remain soluble - a chaotropic crystallization agent (on the extreme end certain high salts, consult Hofmeister for chaotropicity) may rip such soluble aggregates apart or at least get them into a conformationally reasonably well defined state. Crystals do appear/transform even from precipitates on occasion. CD will tell you about the (secondary structure) folding state, not the aggregation state, DLS/MALS would give an estimate for and distribution of the aggregation state. With light scattering, you can also do some systematic experiments exploring what might reduce the aggregate size. I think soluble, defined secondary structure, and a lot of it, is already a good sign. BR On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam r...@brandeis.edu wrote: Hi Folks, As crazy as it sounds, if you have crystallized and managed to solve the structure of a protein from aggregated protein, please could you share your experience. After many constructs, many many expression schemes and after the usual rigmarole of optimization that is also often discussed on ccp4bb (buffers, glycerol, salt concentrations, pH, detergent, additives etc.), I now have a decently expressing truncated construct for my protein (80 kDa) that is pure but aggregated (elutes in the void volume from a Superdex200 column). I am tempted to make a boatload of aggregated protein and set up some crystal trays (after perhaps testing by CD). So I'd like to hear from folks who have been successful in solving structures from aggregates when many many known and tested optimization methods still leave one with aggregated protein. Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Bond Length Outliers (correction)
Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bond Length Outliers (correction) Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't distort anything, it should make it, cough, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- -- -- -- *From: *Bernard D. Santarsiero b...@uic.edu *To: *Greg Costakes gcost...@purdue.edu *Sent: *Thursday, February 16, 2012 11:42:55 AM *Subject: *Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- --
Re: [ccp4bb] Choice of wavelength
For MIR, you also need to weigh your options. If you want to use anomalous signal for SIRAS/MIRAS, you may want to be above the most prominent or at least a useful edge of your HA. On the other hand, being above an HA edge increases you chance of serious radiation damage. Sometimes you may need to back-soak. For light atoms, higher energy generally means less absorption. All depends on many details which you do not provide. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa H. Hsu Sent: Monday, February 13, 2012 1:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Choice of wavelength Hi all. When collecting data, is there a specific wavelength to be chosen at synchrotron source? Does it make difference between 0.9 and 1.5 A, for example? I know it is important for SAD/MAD but how about MIR? Thank you. Theresa
Re: [ccp4bb] problem with coot install
It might be worthwhile to follow the thread of similar problems on the coot mailing list and a generic solution on the coot-wiki, like http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example:_in stalling_a_64bit_nightly_CentOS5_binary_build_on_64bit_SL6.1 BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Emsley Sent: Monday, February 13, 2012 1:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] problem with coot install On 14/02/12 08:17, Alexander U. Singer wrote: Hi -- I was installing the latest version of CCP4 6.2.0 on my machine which uses Linux Fedora Core 5. When downloading the CCP4 package, I used the 'generic linux (x86) option'. The package contains an package for Coot v 0.6.2 which I tar'ed and uncompressed, but when I try to run it, I get this error ./coot-real ./coot-real: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory ./coot: line 254: 16409 Floating point exception$COOT_PREFIX/bin/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real $* Do you know how I can overcome this problem? I guess you need to install the library. For me it's in the following package glib2-devel-2.28.8-1.fc15.x86_64. Either that, or you need a binary that has older dependencies. It's unusual for an .so not to be a link (used by developers). I am surprised that the binary you are using is linked to an .so. FC5 is pretty ancient these days. Paul.
Re: [ccp4bb] Molecular Transform Superimposed on a Dataset
I found a free program that can be used to quickly play with molecule image FFTs. Install Jimage http://rsbweb.nih.gov/ij/ Load for example my image http://www.ruppweb.org/images/transparent_molecule.gif into Jimage Select FFT, select option complex FFT, and execute. Zoom in to the center a few times, and you get a real coarse pixelated image that looks like my transform. I recall having to scale the FFT range when F90 hardcoding the FT which I used to calculate the raw data which were then contour-plotted in Mathcad. Note that the resulting FFT has 2 parts (use the slider on the bottom), the real part is always centrosymmetric, while the complex (phase) part is not. Probably needs some tweaking to be really useful for presentation purpose. BR -Original Message- From: Bernhard Rupp (Hofkristallrat a.D.) [mailto:hofkristall...@gmail.com] Sent: Friday, January 06, 2012 12:35 PM Subject: Re: Molecular Transform Superimposed on a Dataset This may give some idea: Illustration of a molecule and its cosine transform: http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-16.htm and sampled by lattice points http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-01_PART3.htm BR
Re: [ccp4bb] B_sol from EDS
Yes, that is about what one would expect. I also checked a few of the extreme outliers, and almost always can come up with a reasonable value. Which does not remove my curiosity regarding the B_sol 70 cutoff and its purpose. Cheers, BR From: Pavel Afonine [mailto:pafon...@gmail.com] Sent: Monday, January 30, 2012 11:33 AM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] B_sol from EDS Hi Bernhard, I just calculated k_sol and B_sol for all PDB entries that - have reflection data available, - I could re-compute the R-factor within 5%, and - R-work30% using a simple cctbx script. Here is what I get: Distribution of k_sol: 0.000 - 0.060 : 27 0.060 - 0.120 : 12 0.120 - 0.180 : 51 0.180 - 0.240 : 182 0.240 - 0.300 : 1770 0.300 - 0.360 : 13819 0.360 - 0.420 : 19731 0.420 - 0.480 : 3039 0.480 - 0.540 : 471 0.540 - 0.600 : 256 Distribution of B_sol: 0.000 - 31.300 : 4349 31.300 - 62.600 : 29425 62.600 - 93.900 : 4578 93.900 - 125.200: 597 125.200 - 156.500: 225 156.500 - 187.800: 84 187.800 - 219.100: 37 219.100 - 250.400: 23 250.400 - 281.700: 10 281.700 - 313.000: 30 It seems like the result of similar exercise done by Fokine and Urzhumtsev (Acta Cryst. (2002). D58, 1387-1392) still holds (see figure 3 on page 1390 there). Pavel On Mon, Jan 30, 2012 at 11:10 AM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Dear All, when I plot bulk solvent B and K extracted from EDS, an improbable and bimodal distribution appears. In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears (B-axis left to right, 0-200). http://www.ruppweb.org/images/b_sol_contour.jpg http://www.ruppweb.org/images/b_sol_surface.jpg According to a quick peak at EDS instructions, it uses the REFMAC flat bulk solvent model throughout for bulk solvent correction. The main peak in fact has the expected distribution, but it seems that the sharp peak at B_sol=70 represents some cut-off that in a certain set of calculations was used. For data mining it would be useful to know where/when these cutoffs were used. Best regards, BR - Bernhard Rupp http://www.ruppweb.org/ -
Re: [ccp4bb] MAD
For the history buffs and crystallographers needing some RR and chill-out,
an interesting historic fiction read about the era of Newton and Leibnitz
and the foundation of the Royal Society is the Baroque cycle by Neil
Stevenson.
http://en.wikipedia.org/wiki/The_Baroque_Cycle
Cryptonomicon, although written before, picks up a descendent of a character
from the Cycle, and can be considered imho the 4th book
http://en.wikipedia.org/wiki/Cryptonomicon
All together ~ 2400 pages. Cheap on Amazon 3rd party. Book a long vacation.
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian
Tickle
Sent: Sunday, January 29, 2012 5:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MAD
Hi Peter
You are right: the location of the prism experiment is most likely the study
at Woolsthorpe, e.g. see
http://www.isaacnewton.org.uk/texts/OfColours7 . Newton was admitted to
Trinity College in 1661 as a 'sizar' (a paid part-time student employed by
the College) but was forced to return to Woolsthorpe (the family home) in
August 1665 (http://www.isaacnewton.org.uk/Chronology)
to continue studying privately, because the University closed temporarily as
a precaution against the Great Plague ('Black Death') which was spreading
outwards from the initial outbreak in this country in the London Docklands
during the summer of that year. He returned to Trinity in 1667 as a Fellow
of the College.
So I should have been more precise and said that Newton performed the prism
experiment during the time that he was associated with Trinity (it's not
clear what the nature of his association with Trinity was during the 2 years
he spent doing experiments at Woolsthorpe).
Cheers
-- Ian
On 28 January 2012 09:35, Peter Moody pcem1bigfi...@gmail.com wrote:
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you
will see a conflicting claim for location of the classic prism
experiment. You will also find an apple tree in the garden, but that is
another story..
Peter
PS this is my special ccp4bb email account, it doesn't always get the
attention it deserves.
On 19 January 2012 17:50, Ian Tickle ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This
is of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it
can be determined by very careful and precise interferometric
experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor,
because the real part of the refractive index is what describes
dispersion (the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it
stemmed from a visit by Wayne Hendrickson to Birkbeck in London some
time around 1990: he was invited by Tom Blundell to give a lecture on
his MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a
misnomer for the reasons I've elucidated above. Wayne liked the MAD
acronym and wanted to keep it so he needed a replacement term
starting with D and diffraction was the obvious choice, and if you
look at the literature from then on Wayne at least consistently
called it multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from
[ccp4bb] CCP4 win dev
Dear ccp4 win developers: I would like to compile Ian's EDSTAT program using my windows7/64 ifort compiler. I have a few questions re library linking and win-compliable source distribution - wonder who I may kindly harass off-board. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] on the electronic density of several maps
You might want to look at some images of side chain electron density. http://www.ruppweb.org/garland/gallery/Ch2/index_2.htm BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dialing Pretty Sent: Friday, January 13, 2012 2:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] on the electronic density of several maps Dear All, For the electronic density of LEU and Pro in the electronic density map, which is much stronger? For the electronic density of LEU and Lys in the electronic density map, which is much stronger? The reason I ask the above questions is I need to distinguish them in the electronic density map. I am looking forward to getting your reply. Fenghui
[ccp4bb] NMR review
Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain?
Re: [ccp4bb] NMR review
Does out of phase imply incoherent scattering? I though it means inelastic Compton scattering? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Thursday, January 12, 2012 1:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR review Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA / RNA molecule that are ?exible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the ?nal electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universit t M nchen Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Molecular Transform Superimposed on a Dataset
This may give some idea: Illustration of a molecule and its cosine transform: http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-16.htm and sampled by lattice points http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-01_PART3.htm BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Friday, January 06, 2012 9:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Molecular Transform Superimposed on a Dataset Actually, as a way to make this type of figure, I think there are programs which output simulated diffraction images, so perhaps I could just input a .pdb file with some really huge (fake) cell parameters (10,000 Ang?), and then the resulting spots would be really close together and approximate the continuous molecular transform. I think this would amount to the same thing as the molecular transform of the model itself--am I right? Does anyone know which software outputs simulated diffraction images? Jacob On Fri, Jan 6, 2012 at 10:25 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, has anyone come across a figure showing a normal diffraction image, and then next to it the equivalent molecular transform, perhaps with one image as phases and one as amplitudes? Seems like it would be a very instructional slide to have to explain how crystallography works (I know about Kevin Cowtan's ducks and cats--I was looking for approximately the same but from protein or NA molecules.) I don't think I have ever seen an actual molecular transform of a protein or NA molecule. All the best, Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] refmac low resolution REMARK
So what's new? Alzheimer's and late night senile dementia :-) BR PS: nice site! -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Monday, January 02, 2012 4:34 AM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] refmac low resolution REMARK Hi Bernhard So what's new? See http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html (17-Nov-11). Cheers -- Ian
[ccp4bb] refmac low resolution REMARK
Dear Developers, it seems to me that at least Refmac 5.6.0117 does not report the actual lowest resolution used in refinement, but instead the lowest resolution of the hkl index range generated by the default cif import script instead. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.63 --- The data go only to 28.66 A according to mtzdump as well as xprep as far as I can tell, cif2mtz does it right and reports * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.001220.25305 ( 28.660 - 1.988 A ) - then the script calls unique which pads the reflections up * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.000670.25302 ( 38.628 - 1.988 A ) - which then propagates to CAD and FREEFLAG into the MTZ header where it is picked up by refmac. OVERALL FILE STATISTICS for resolution range 0.001 - 0.253 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC-16 16 0 100.00 0.1 6.3 38.63 1.99 H H 2 NONE 0 28 0 100.00 10.5 10.5 38.63 1.99 H K 3 NONE 0 19 0 100.00 7.3 7.3 38.63 1.99 H L 4 NONE0.0 9.0 0 100.00 4.50 4.50 38.63 1.99 I FREE 5 NONE7.7 707.8 361 96.40 102.76 102.76 28.66 1.99 F FP - this is the right number! 6 NONE1.637.3 361 96.40 8.84 8.84 28.66 1.99 Q SIGFP I have noticed that other PDB/sf file sets (not mine) seem to be affected as well. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] refmac Bsol
Dear Garib, thank you for the quick response despite (or because of) the holidays. Ill try to summarize because I am not sure I understand yet, and it might be useful for all : Ø Partial structure mask bulk solvent parameters. Mask bulk solvent B value is in addition to protein B value. Not quite clear what you are saying here how does that answer what the Overall means versus the Partial? (some guessing below) Ø Full scaling is like this: Fscaled = scale_protein exp(-B s^2/4) exp(-s^T U s) (F_protein + scale_mask exp(-B_mask s^2/4) Fmask) (1-scale_babinet exp(-B_babinet s^2/4)) Ok then I see that I can use either _mask or _babinet terms because only one set of terms is in effect if the other one is zero. If I turn both off, I get basic k, B scaling, plus anisotropic B correction. Makes perfect sense. Based on that I will try to determine which line in the printout is actually the bulk solvent contribution. For the Partial structure part: Partial structure1: scale =0.375, B = 24.388 If I recall correctly, for the flat bulk solvent model the scale_mask and B_mask are generally in the order of 0.4 and 40AA, so then this ought to be scale_mask and B_mask of the solvent contribution? Yes? No? Now for Overall : scale =0.891, B = -0.266 Now it gets interesting: what is this in terms of the above equation? I dont seem to be able to factor out a single overall scale and B correction from your eqn, but it sure looks like a correction term from bulk to be applied to the overall k and B . Can you clarify please? Ø Current version of refmac does not calculate Wilson B value I think we can get that readily from say truncate. But that wont be in the PDB REMARK 3 then Ø Note: Overall Bvalue may correspond to residual overall B value if you are using TLS refinement Understood. Ø If you use simple scaling then mask solvent is still on. Yes that is consistent with the doc. Ø You can turn it off by Calculate the contribution of from the solvent region Yes, that can be done by unclicking the box Calculate the contribution from the solvent region. Handy if one needs to check certain things Ø To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. Yep, understood. Thx, BR From: Garib Murshudov [mailto:garib.murshu...@gmail.com] On Behalf Of Garib N Murshudov Sent: Thursday, December 29, 2011 4:47 PM To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refmac Bsol Partial structure mask bulk solvent parameters. If you use simple scaling then mask solvent is still on. You can turn it off by Calculate the contribution of from the solvent region To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. I hope it helps regards Garib
[ccp4bb] refmac Bsol
Dear Refmac developers group,
I am trying to understand a small detail in the refmac log listing. In the
bulk
solvent section just below the restraint table (I use monitor MANY in
general):
-
Overall : scale =0.891, B = -0.266
Partial structure1: scale =0.375, B = 24.388
Overall anisotropic scale factors
B11 = -0.39 B22 = 0.09 B33 = 0.33 B12 = -0.00 B13 = 0.48 B23 = 0.00
-
Is the listing indeed containing the flat bulk solvent model ('simple model'
in refmac gui, SOLVENT YES) k and B in the first 2 lines?
If so, I am curious
a) what exactly is 'Overall' versus 'partial structure'? What is the
relative magnitude of the scale and B telling me in each case?
b) would it not be useful to have it reported in the PDB header?
All I find there is the anisotropic B scaling matrix and a
mean (overall) B value (of unspecified origin - how exactly is that
computed?)
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711
Explanation/intuition would be much appreciated.
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
hofkristall...@gmail.com
b...@hofkristallamt.org
http://www.hofkristallamt.org/
--
Old and treacherous will beat young and skilled every time
--
PS: The doc leaves me a little confused because SCAL type SIMP would imply
KB = K0*exp(-B0*s^2) (Simple Wilson scaling)
i.e. K1 = 0
while BULK (Babinet) which I did not specify
KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2))
gives me 2 Ks and Bs.
So I conclude that 'overall' and 'partial' lines do not list Babinet ks and
Bs (the B is also too small for that)
[ccp4bb] cif_mmdic.lib
Dear Developers, A few observations during data import/export ccp4i win 64 installed from ccp4-6.2.2.msi a) cif2mtz 6.2 says: CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) (Raised in zzs_undump) Cannot open file C:\CCP4\6.2\lib\data\cif_mmdic.lib for reading! This file is in C:\CCP4\6.2\lib and not in C:\CCP4\6.2\lib\data - copying it there fixes the problem. b) in 'Convert from MTZ', selecting SHELX as format, the HKL extension shows up twice, plus a comma, in the HKLOUT gui line r3k78sf.hkl,.HKL c) Question: any particular reason why the cell parameters and SG are not read from the mmcif and need to be entered by hand? d) is it normal that the header in the GUI window says 'CCP4 Program Suite 6.2.0 CCP4Interface 2.1.0 runing on .' when I install 6.2.2 ? Or did something go wrong? Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
[ccp4bb] OT: LN2 autofill
Hi Fellows, I am looking for some advice re LN2 autofill. I want to automatically refill an open special-use foam Dewar on the crystal harvesting robot from an unpressurized secondary storage Dewar. We found this system http://www.norhof.com/fillingexample.html and it seems to do what we need and also seems reasonably priced (little more than 5k) plus shipping from Europe. I wonder if someone has experience with US available alternatives or finds some gotcha I missed... Maybe off-board if considered mission creep... Best regards, BR - Scientists are there to find the laws of nature. Engineers are there to work around them. -
Re: [ccp4bb] bias removal server
I am not sure this service is maintained anymore, but given that with automated model building pretty much the same can be achieved nowadays (pus benefit of a model), the ARP/wARP server in Hamburg is a well-working and up-to-date alternative. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, December 20, 2011 10:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] bias removal server Dear All, Any of you know if the Bias removal server at http://tuna.tamu.edu/ works? My friend says that 'may be the server doesn't exist' as he never heard back from them about login info. Thanks Rajesh
[ccp4bb] Vote for Bill !
Hi Fellows, here is your chance to vote for a crystallographer in the People's Choice education program contest: http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881id=485f01c36b; e=76452e4682 Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] Movements of domains
If the difference in likelihood is quite small then you cannot distinguish between a RB shifted model and one w/o the shift and that shift must be insignificant (in a statistical sense.) If the likelihood is better when the shift is allowed then the shift is significant. That of course is correct and leads to the interesting (and in part previously discussed) question how to quantify (log) likelihood ratios in terms of significance. I am not sure that this is trivial. More likely better, very likely better, kinda really likely better? Having said that I also want to caution the normal distribution statistical test fans, who think that a p value or similar has any more meaning. Whether p=0.05 means something (other than a statistical metric) is equally fuzzy; it just conveys a false sense of precision and erudition. May I quote: The scientist must be the judge of his own hypotheses, not the statistician. A.F.W. Edwards (1992) in Likelihood - An account of the statistical concept of likelihood and its application to scientific inference , p. 34. Brrr On 11/21/11 14:52, Filip Van Petegem wrote: Hello Jacob, that's correct, I'm only looking at the mathematical significance, not the biological one. I follow the same reasoning - it is highly improbably for all atoms to be skewed in the same direction. In a case I'm currently looking at, I'm particularly dealing with cryo-EM data, not X-ray structures, but with the same underlying principles: what are the odds that all pixels of the map move together in the same direction? As mentioned for X-ray structures, a Luzzati analysis may give information about the positional errors, but there should be an increased resolution when comparing domain movements, because it's unlikely for all atoms to have an error in the same direction. Filip On Mon, Nov 21, 2011 at 2:16 PM, Jacob Keller j-kell...@fsm.northwestern.edu mailto:j-kell...@fsm.northwestern.edu wrote: Just to clarify: I think the question is about the mathematical sense of significance, and not the functional or physiological significance, right? If I understand the question correctly, wouldn't the reasoning be that admittedly each atom in the model has a certain positional error, but all together, it would be very unlikely for all atoms to be skewed in the same direction? Jacob On Mon, Nov 21, 2011 at 4:04 PM, Filip Van Petegem filip.vanpete...@gmail.com mailto:filip.vanpete...@gmail.com wrote: Dear crystallographers, I have a general question concerning the comparison of different structures. Suppose you have a crystal structure containing a few domains. You also have another structure of the same, but in a different condition (with a bound ligand, a mutation, or simply a different crystallization condition,...). After careful superpositions, you notice that one of the domains has shifted over a particular distance compared to the other domains, say 1-1.5 Angstrom. This is a shift of the entire domain. Now how can you know that this is a 'significant' change? Say the overall resolution of the structures is lower than the observed distance (2.5A for example). Now saying that a 1.5 Angstrom movement of an entire domain is not relevant at this resolution would seem wrong: we're not talking about some electron density protruding a bit more in one structure versus another, but all of the density has moved in a concerted fashion. So this would seem 'real', and not due to noise. I'm not talking about the fact that this movement was artificially caused by crystal packing or something similar. Just for whatever the reason (whether packing, pH, ligand binding, ...), you simply observe the movement. So the question is: how you can state that a particular movement was 'significantly large' compared to the resolution limit? In particular, what is the theoretical framework that allows you to state that some movement is signifcant? This type of question of course also applies to other methods such as cryo-EM. Is a 7A movement of an entire domain 'significant' in a 10A map? If it is, how do we quantify the significance? If anybody has a great reference or just an individual opinion, I'd like to hear about it. Regards, Filip Van Petegem -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 tel:%2B1%20604%20827%204267 email: filip.vanpete...@gmail.com mailto:filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] weight matrix and R-FreeR gap optimization
What is your resolution? The gap is usually wider at lower resolution. Here a figure displaying distribution gap stats: http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp hy_Fig_12-24.htm Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Tuesday, November 08, 2011 8:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] weight matrix and R-FreeR gap optimization On 11/08/2011 05:39 AM, james09 pruza wrote: Dear ccp4bbers, I wonder if someone can help me defining proper weight matrix term in Refmac5 to lower the R-FreeR gap. The log file indicates weight matrix of 1.98 with a gap of 7. Thanks for suggestions in advance. James What is your resolution? The gap is usually wider at lower resolution. Eleanor
Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong
If for example your presumed coil is differently bent than your search probe, overall rmsd is high and MR will likely fail. But maybe ARCIMBOLDO with helix fragments might do at 1.65A? George or Isabel will have a better answer. Good luck, BR PS: And may San Matheus de las Coefficientes listen to your prayers... :-) -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Napoleão Valadares Sent: Monday, October 17, 2011 10:09 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong Hi there! I got crystals from some synthetic peptides I bought, they are 30 residues long and are supposed to form a coiled coil. I collected various data sets (home source, Brookhaven and Diamond), including some at the resolution of 1.65 A, for which the space group appears to be C222 or C2221. The unit cell is small, 22.67, 88.06, 26.13, and the Matheus Coefficient indicates that's there's only one helix in the asymmetric unit and a 25% solvent content. I have tried A LOT of Molecular Replacement using Phaser and Phenix AutoMR. I'm using a 80% identity coiled coil helix as search model. The programs give me solutions with reasonable maps, but it is never possible to refine to achieve Rvalues below 0.40. Additionally, maps from different solutions look reasonable, so I'm thinking these are all bias. I have 5 other synthetic 30 residues peptides (that crystallize in different space groups and diffract to lower resolutions), including a SelenoMethionine (SM) derivative (but it does not have enough anomalous signal, ASU is too big, it is possible that the SM are disordered). I'm stuck on this since March. Regarding the search model, I already tried trimming some or all side chains and removing 2, 3 or 5 residues on each/both sides. I also tried other search models. Maybe some magic combination of parameters on Phaser or other programs can help me. What is your advice regarding how to proceed with MR? Is there some program, procedure, parameter, pray or human sacrifice that could help me? Thank you. Regards, Napo
Re: [ccp4bb] IUCr committees, depositing images
Hi Fellows, I was attending the inaugural meeting of the Data Deposition Working Group in Madrid. They are aware of the various points raised, and a document/recommendation has been prepared that I assume will be soon made public (John?). Amount of data seems not an insurmountable technical problem. The most important point is that the data are getting consistently better and contain more information than we currently make use of. Just think of diffuse solvent contributions, commensurate and incommensurate superstructures, split reflections, and similar stuff that presently just gets indexed away. Better data processing software will certainly be developed and will provide a better data model, ultimately allowing better structure models. At the same time, almost all forgery issues disappear automatically as an added (but imho minor) bonus. Cheers, BR PS: on a cynical note, what makes one believe that data processing is carried out at any higher level of competency than say the refinement? The only comfort here is that when it is done immediately by the beamline fellows, it is probably done well. In any case, maybe REPROCESS_PDB is the thing of the future. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Sunday, October 16, 2011 12:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] IUCr committees, depositing images One other question (for both key issues described): what exactly is the problem the committees are aiming to address? Because I can't help noticing that Tom's email did not spark an on-list discussion; do people actually feel either are issues? Isn't the more burning problem how best to use the 10,000s of structures we're churning out? In the grand scheme of things, they're pretty inaccurate anyway: static snapshots of crippled fragments of proteins far from their many interaction partners. So do we need 100,000s of structures instead? If so, we may soon (collectively) stop being able to care about the original dataset or how to reproduce analysis number 2238 from 2 years ago. (No, I'm not convinced this question is relevant only to structural genomics.) phx. On 16/10/2011 19:38, Frank von Delft wrote: On the deposition of raw data: I recommend to the committee that before it convenes again, every member should go collect some data on a beamline with a Pilatus detector [feel free to join us at Diamond]. Because by the probable time any recommendations actually emerge, most beamlines will have one of those (or similar), we'll be generating more data than the LHC, and users will be happy just to have it integrated, never mind worry about its fate. That's not an endorsement, btw, just an observation/prediction. phx. On 14/10/2011 23:56, Thomas C. Terwilliger wrote: For those who have strong opinions on what data should be deposited... The IUCR is just starting a serious discussion of this subject. Two committees, the Data Deposition Working Group, led by John Helliwell, and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su) are working on this. Two key issues are (1) feasibility and importance of deposition of raw images and (2) deposition of sufficient information to fully reproduce the crystallographic analysis. I am on both committees and would be happy to hear your ideas (off-list). I am sure the other members of the committees would welcome your thoughts as well. -Tom T Tom Terwilliger terwilli...@lanl.gov This is a follow up (or a digression) to James comparing test set to missing reflections. I also heard this issue mentioned before but was always too lazy to actually pursue it. So. The role of the test set is to prevent overfitting. Let's say I have the final model and I monitored the Rfree every step of the way and can conclude that there is no overfitting. Should I do the final refinement against complete dataset? IMCO, I absolutely should. The test set reflections contain information, and the final model is actually biased towards the working set. Refining using all the data can only improve the accuracy of the model, if only slightly. The second question is practical. Let's say I want to deposit the results of the refinement against the full dataset as my final model. Should I not report the Rfree and instead insert a remark explaining the situation? If I report the Rfree prior to the test set removal, it is certain that every validation tool will report a mismatch. It does not seem that the PDB has a mechanism to deal with this. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] IUCr committees, depositing images
As in reprocess completely from images, I meant. From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Sunday, October 16, 2011 1:31 PM To: hofkristall...@gmail.com Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] IUCr committees, depositing images Wasn't that already implemented in Phenix ? Jürgen On Oct 16, 2011, at 4:20 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: REPROCESS_PDB .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] IUCr committees, depositing images
Ø Do you mean to reprocess determination of I and sig(I) from the diffraction images automatically??? Or just to get an access to the raw data? Reprocessing the images with the to-be-developed new software that will process the information in the data in full, and then using the new-and-improved refinement software to automatically refine a physically more realistic model. Sounds far-fetched now but will happen soon, in the cloud of bored petaflop iphones 8, each with 32 TB of memory . Cheers, BR
Re: [ccp4bb] IUCr committees, depositing images
Ø Not if you are interested in scattering that falls between reciprocal lattice maxima, or if you want to preserve the possibility of applying future data reduction packages. Yep, this is exactly what I expressed in my original statement: diffuse solvent contributions, commensurate and incommensurate superstructures, split reflections, and similar stuff that presently just gets indexed away BR
Re: [ccp4bb] EDS server
it will be before we all travel to work with jetpacks or flying cars http://www.popularmechanics.com/science/4247253 Thunderbolt Aerosystems, based in California, plans to start selling its ThunderPack TP-R2G2 rocket belt to customers this summer. http://www.popularmechanics.com/technology/aviation/news/terrafugias-flying- car-clears-regulatory-hurdles The Terrafugia company now plans to fly the production prototypes next March.. :-) BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Friday, September 02, 2011 7:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] EDS server Hi all, Simple question, is there a way I can upload my own data into the EDS server? I see only place for it to take from data already published in the PDB. First of all, if you deposit at PDBe, EDS will be run on your deposition and you can access the results after annotation. Second, RCSB operates a validation server that carries out similar calculations and which you can use prior to deposition. Having said that, yes, there is actually an *unsupported* version of EDS to which you can upload your model and structure factors (MTZ or CIF file). Note that it is unsupported, unofficial, unmaintained, buyer beware and your mileage may vary. In the future, there will of course be a shiny new wwPDB X-ray validation server which will include EDS-style calculations. (I won't make any promises as to when, but it will be before we all travel to work with jetpacks or flying cars.) --Gerard PS: If you want to try out the *unsupported* etc. PRedeposition EDS server (PREDS), throw your browser at http://eds.bmc.uu.se/eds/preds.php (but read http://eds.bmc.uu.se/eds/preds_help.html first). ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] Another paper structure retracted
the editor should agree to publish the paper swiftly in advance before the data become accessible to reviewers. This seems to miss the point - how is the reviewer then supposed to judge the map? BR Nian On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7 http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%2362 69%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y _acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa24 3dc98e395b6ac590d , 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 tel:%2B1%20604%20827%204267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
