Re: [ccp4bb] images
I started a poll to find out whether crystallographers need and are interested in an X-ray diffraction data bank. Will crystallographers find this resource helpful and be willing to submit their structures? I hope you will take a moment to share your opinion via the poll and/or by posting any questions or comments you may have. I will follow up with results in about a month. http://www.p212121.com/2009/06/04/do-we-need-an-x-ray-diffraction-image-data-bank/ Thanks. Sean Seaver
Re: [ccp4bb] images
Hi Sean Ash Buckle has already developed one! Tools for general deposition will be released shortly. http://tardis.edu.au/ Cheers J Sean Seaver s...@p212121.com wrote: I started a poll to find out whether crystallographers need and are interested in an X-ray diffraction data bank. Will crystallographers find this resource helpful and be willing to submit their structures? I hope you will take a moment to share your opinion via the poll and/or by posting any questions or comments you may have. I will follow up with results in about a month. http://www.p212121.com/2009/06/04/do-we-need-an-x-ray-diffraction-image-data-bank/ Thanks. Sean Seaver -- Professor James Whisstock ARC Federation Fellow Honorary NHMRC Principal Research Fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
Re: [ccp4bb] images
I would be against the storage of crystals due to a number of reasons. 0) Crystal is harder to be fake than images; From crystal to images, maybe only 1 hour needed; -would be worried about: proper handling of crystals after data collection, ice formation, dropping, remounting if it another future collection is warranted, etc... 1) Protein crystals could be stored in LN2 for probably more than 1000 years; -systems and staff (cost) would need to be developed to maintain the system 2) There normally are small and not a big space occupier; -either are flash drives 3) They can be easily maintained by simply feed LN2 and controled by computer; -development of equipment, robotics and programming (cost) 4) You do not need buy hard drives, DVDs, .. and no need in suffering from different format of files, ... -disk space is cheap and becoming cheaper 5) Crystallography keeps moving forward though slow. It is possible that future people can get better data from the almost same crystal, better than using softwares to deal with images, ... -it is possible, but feel that the data being collected today is yielding reasonable conclusions when assessed correctly by the author 6) Temporarily I suggest the generous 3rd generation synchrotron facilities round out some space for saving those crystals, because there are normally located far from downtown and have enough land around... -this would take years 7) ... Ted www.P212121.com
Re: [ccp4bb] images
4) You do not need buy hard drives, DVDs, .. and no need in suffering from different format of files, ... -disk space is cheap and becoming cheaper And what about different format of pucks/cassettes/tongs etc? I can still read my old Vax backup tapes (on a linux box with an exabyte tape drive), but my old Yale-style pins won't fit in the Hampton Research cryotongs available at the beamline, they don't sit well on the standard goniometer magnet, and can't be picked up by the automounter. Ed
Re: [ccp4bb] images
Kay Diederichs wrote: In this case the structure factors were deposited, but these do not have a column for the anomalous signal. Re-refinement with these structure factors was inconclusive. If I could have downloaded the images, I could have investigated this easily, because there's a large difference in the f of those two metals. So to me access to images sometimes may help to answer a scientific question. I would add a plea to those considering an image deposition system: accept MAPS too! At the very least it would be nice to see the initial and final maps the crystallographer used. Even if I have the structure factors I'm not necessarily an expert on the ins and outs of what someone had to do to refine a twinned or otherwise troublesome structure, and I don't want to have to learn the specific refinement program you used to be able to reproduce the exact map you saw. (For very old structures, it may no longer be possible to compile the specific version of the refinement software on new processors/OSes, or someone may have used a commercial refinement package.) And of course, there are non-crystallographers who use structures and it is absurd to expect them to learn x-ray refinement to see the relevant map for a twinned structure that EDS couldn't process. I love EDS. But even though it usually has a map for a given structure, seeing the actual map generated by the crystallographer who was the expert on the project would be better. Once a system is designed that is large enough to handle images, maps would not significantly increase the required storage space. I've poked a couple people to suggest that even now the PDB ought to be accepting maps. -- -Eric
Re: [ccp4bb] images
Now that there is possibility that images could be fake, which means the first and automatic FFT in crystallography could be falsified. All those depositions later than this would be just nothing but wrong, if images were fake. To keep the first and most important FFT not contaminated, I would suggest the deposition of crystals. 0) Crystal is harder to be fake than images; From crystal to images, maybe only 1 hour needed; 1) Protein crystals could be stored in LN2 for probably more than 1000 years; 2) There normally are small and not a big space occupier; 3) They can be easily maintained by simply feed LN2 and controled by computer; 4) You do not need buy hard drives, DVDs, .. and no need in suffering from different format of files, ... 5) Crystallography keeps moving forward though slow. It is possible that future people can get better data from the almost same crystal, better than using softwares to deal with images, ... 6) Temporarily I suggest the generous 3rd generation synchrotron facilities round out some space for saving those crystals, because there are normally located far from downtown and have enough land around... 7) ... Lijun Kay Diederichs wrote: In this case the structure factors were deposited, but these do not have a column for the anomalous signal. Re-refinement with these structure factors was inconclusive. If I could have downloaded the images, I could have investigated this easily, because there's a large difference in the f of those two metals. So to me access to images sometimes may help to answer a scientific question. I would add a plea to those considering an image deposition system: accept MAPS too! At the very least it would be nice to see the initial and final maps the crystallographer used. Even if I have the structure factors I'm not necessarily an expert on the ins and outs of what someone had to do to refine a twinned or otherwise troublesome structure, and I don't want to have to learn the specific refinement program you used to be able to reproduce the exact map you saw. (For very old structures, it may no longer be possible to compile the specific version of the refinement software on new processors/OSes, or someone may have used a commercial refinement package.) And of course, there are non-crystallographers who use structures and it is absurd to expect them to learn x-ray refinement to see the relevant map for a twinned structure that EDS couldn't process. I love EDS. But even though it usually has a map for a given structure, seeing the actual map generated by the crystallographer who was the expert on the project would be better. Once a system is designed that is large enough to handle images, maps would not significantly increase the required storage space. I've poked a couple people to suggest that even now the PDB ought to be accepting maps. -- -Eric
Re: [ccp4bb] images
On Mar 19, 2009, at 3:26 AM, Andrew Purkiss-Trew wrote: On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote: Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... As far as I know, most detectors write the current time into the image header. Certainly our in house MAR image plate systems do, as do the detectors at Diamond and ESRF (for those that I've looked at this morning). FYI at my beamline (ALS 12.3.1), in addition to the usual useful metadata, we also put in the beamline ID and the serial number of the detector. In theory anything can be added if you take the time to customize the detector code. HEADER_BYTES= 512; DIM=2; BYTE_ORDER=little_endian; TYPE=unsigned_short; SIZE1=3072; SIZE2=3072; PIXEL_SIZE=0.102592; BIN=2x2; BIN_TYPE=HW; ADC=fast; CREV=1; BEAMLINE=ALS1231; DETECTOR_SN=907; DATE=Tue Feb 3 11:07:38 2009; TIME=10.00; ACC_TIME=11516; DISTANCE=649.80; TWOTHETA=0.00; PHI=191.310; OSC_START=191.310; OSC_RANGE=1.000; WAVELENGTH=1.033184; BEAM_CENTER_X=155.70; BEAM_CENTER_Y=157.40; DENZO_X_BEAM=157.76; DENZO_Y_BEAM=155.70; Scott
Re: [ccp4bb] images
Jacob, Just for the fun, and for historical exactness... I would rather invoke Laplace for such an argumentation, whereas Poincaré should better be invoked for a very strong warning against it. Therefore, ignoring the warning and following Laplace, we could even readily extend your suggestion from back-calculating the images to solving the corresponding structures (and thus also writing the corresponding papers). And write The End (as nauseam, of course ::)) Philippe Dumas Jacob Keller a écrit : Perhaps we could use Poincare's argument(?), that knowing one cross section of the universe in all of its detail would allow forward and back-calculation of all previous states. Then the universe would be its own lab notebook/ archive, and we would not need to bother with all of these technicalities in the first place. The images, then, could be back-calculated from the current (or any) configuration of all the universe's atoms, and then we could work better on improving our crystallography software (and ferreting out fraud) from those... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** begin:vcard fn:Philippe Dumas n:Dumas;Philippe org:CNRS;Biophysique et Biologie Structurale adr;quoted-printable:15 rue Ren=C3=A9 Descartes;;IBMC;Strasbourg;;67084;France email;internet:p.du...@ibmc.u-strasbg.fr title:Directeur de Recherche tel;work:+33 (0)388 41 70 02 tel;fax:+33 (0)388 60 22 18 url:http://www-ibmc.u-strasbg.fr/arn/Dumas/index_dum_fr.html version:2.1 end:vcard
Re: [ccp4bb] images
On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote: Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... As far as I know, most detectors write the current time into the image header. Certainly our in house MAR image plate systems do, as do the detectors at Diamond and ESRF (for those that I've looked at this morning).
Re: [ccp4bb] images
Hi Frank, I would have assumed that the purpose of the experiment would have been defined in the publication associated with the deposition - not to trivialize your point, which is very important, but to put it in context. I would also assume that the sequence and ligands are as per the associated PDB deposition. So so far we are quite a way towards being able to get something useful from this data with what we have already. The relationship to associated data sets - this is harder, certainly, but not impossible. In particular, how frequently is it the case that the measurements from these 15 similar data sets actually contribute directly to the structure solution? Obviously there is a process as defined in a lab book, but you could take the stance, at least in the first instance, that they do not directly contribute if the same conclusions would be reached in their absence. Obviously any repository must be more than an FTP site, and must allow the scientific links between structures and data to be made (for example including the model used for the successful molecular replacement.) It does seem clear to me though that we cannot set up the perfect repository in the first instance, but we do have to start somewhere. Perhaps we do not need the right answer, but one which is less wrong that not making available the data at all? Just my thoughts on this. Cheers, Graeme 2009/3/18 Frank von Delft frank.vonde...@sgc.ox.ac.uk: Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... phx Gerard Bricogne wrote: Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
Re: [ccp4bb] images
Dear Bernhard, Thank you for this suggestion. The question is: who outside the US can be in? I would be most happy to contribute to arguing the scientific case (in the broadest sense) for the benefits of such an initiative, and to play whatever role I can in getting (other people to put ...) the nuts and bolts in place. Could you broadcast the information about this kind of grant? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 04:24:18PM -0700, Bernhard Rupp wrote: All right: How about then putting in a NIH challenge grant (due April 27) for image archiving? Who is in? BR -Original Message- From: Gerard Bricogne [mailto:g...@globalphasing.com] Sent: Wednesday, March 18, 2009 4:12 PM To: Bernhard Rupp Cc: 'Gerard Bricogne'; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, Re-reading your previous message, I can see that I did indeed misread it, and I apologise for that. Perhaps it was the expression put to rest in relation to a topic where so much action is needed that made me charge in the wrong direction. Although this thread is now attracting additional suggestions about what else it might be a good thing to archive, this should not result in a dilution of the urgency of this particular item. As for the argument that any new task can only be done if there is extra money, then isn't this the ideal time to argue that we need a PDB stimulus package? After all, the PDB is a bank ... . With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 12:14:29PM -0700, Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd
Re: [ccp4bb] images
Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results.
Re: [ccp4bb] images
Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results.
Re: [ccp4bb] images
On Wednesday 18 March 2009 17:04:49 Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? Apparently so: http://www.dclunie.com/medical-image-faq/html/index.html :-) . -- Dr. ir. Lieven Buts, Postdoctoral Fellow Structural Biology Brussels, Vrije Universiteit Brussel Department of Cellular and Molecular Interactions, VIB
Re: [ccp4bb] images
Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results.
Re: [ccp4bb] images
Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results.
Re: [ccp4bb] images
On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote: Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? Overlooked superlattice? Incorrect point group assignment? Failure to recognize a non-merohedral twin? Thermal diffuse scatter? Subsequent improvements in integration programs? Ethan regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] images
Hi Garib Does this answer your question (see final paragraph): http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html Best -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Garib Murshudov Sent: 18 March 2009 16:42 To: Herbert J. Bernstein Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] images Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] images
Dear CCP4BB, For further research of a particular structure wouldn't hints on expressing, purifying and crystalizing the protein often be more useful than images or amplitudes? Liz On 18 Mar 2009, at 17:00, Ethan Merritt wrote: On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote: Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? Overlooked superlattice? Incorrect point group assignment? Failure to recognize a non-merohedral twin? Thermal diffuse scatter? Subsequent improvements in integration programs? Ethan regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] images
As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
Re: [ccp4bb] images
Hi I've heard of a tool from the Golden State which could (potentially) be used for forging diffraction images... I believe it's called mlfsom. On 18 Mar 2009, at 17:50, Felix Frolow wrote: One convincing argument I have: We will be able to catch fraud ultimately. Fraud is a devastation for structural biology. ...Unless they will be smart enough to forge diffraction data images, not a big deal. The second one - in the case of a controversy of the deposited results (possible thing) we can try to re-interpret the space group and Bravais lattice And one more, when we have time we can show that we know better to process and to refine ;-) Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Mar 18, 2009, at 6:41 PM, Garib Murshudov wrote: Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] images
There have been excellent examples given for cases in which the original data would have been very valuable for discussion and understanding. However, it has always been my understanding that scientists are required to keep the original data on which their conclusions are based. It is also my understanding that (in the US) from this logical requirement there is a legal requirement for scientists to keep their original research data on file. This presumably is imposed by the granting agancies, although I have to admit that I have actually never read this rule in writing anywhere. The question is not 'should it be kept', the question is 'how long should it be kept'. It is self-evident that all data are kept for at least 5 years (about the time it takes to get a student to graduate). Should it be 10 years? Should it be 15-20 years? In practice, I think the answer is that when everyone who can remember doing the project has gone (PI retires), then the data are no longer useful because nobody can remember what?they are?for.?I would reluctantly type rm -f * in that case. In addition to this discussion one would have to consider 'should ALL data be preserved'? We all know that it usually?takes more than one diffraction experiment to get a structure. Is it OK to discard the data sets (images) that were not used? My somewhat arbitrary answer is ALL data should be preserved. It is like your lab notebook - do you preserve data on unsuccessful cloning and expression? Yes, you do because you never know what you can learn from this. And also, your unsuccessful ! experiments together with?the successful ones form the record how you?came to an answer/conclusion.?There are recent questions in literature and on this bb that could be answered if we had the next best data set. ? Mark? -Original Message- From: Garib Murshudov ga...@ysbl.york.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 18 Mar 2009 10:41 am Subject: Re: [ccp4bb] images Dear all? ? Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels).? ? Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images?? ? regards? Garib? ? ? On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote:? ? Actually the radiologists who manage CT and PET scans of brains do have? a solution, called DICOM, see http://medical.nema.org/. If we work? together as a community we should be able to do as well as the? rocket scientists and the brain surgeons' radiologists, perhaps even? better. -- Herbert? ? =? Herbert J. Bernstein, Professor of Computer Science? Dowling College, Kramer Science Center, KSC 121? Idle Hour Blvd, Oakdale, NY, 11769? ? +1-631-244-3035? y...@dowling.edu? =? ? On Wed, 18 Mar 2009, Jacob Keller wrote:? ? Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution?? ? JPK? ? ***? Jacob Pearson Keller? Northwestern University? Medical Scientist Training Program? Dallos Laboratory? F. Searle 1-240? 2240 Campus Drive? Evanston IL 60208? lab: 847.491.2438? cel: 773.608.9185? email: j-kell...@northwestern.edu? ***? ? - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be ? To: CCP4BB@JISCMAIL.AC.UK? Sent: Wednesday, March 18, 2009 5:36 AM? Subject: Re: [ccp4bb] images? ? ? Herbert J. Bernstein wrote:? Other sciences have struggled with this and seem to have found an answer.? Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html? kind regards,? Klaas? ? This is a good time to start a major crystallogrpahic image? archiving effort. Money may well be available now that will not be? avialable six month from now, and we have good, if not perfect,? solutions available for many, if not all, of the technical issues? involved. Is it really wise to let this opportunity pass us by?? The deposition of images would be possible providing some consistent? imagecif format was agreed.? This would of course be of great use to developers for certain? pathological cases, but not I suspect much value to the user? community - I down load structure factors all the time for test? purposes but I probably would not bother to go through the data? processing, and unless there were extensive notes associated with? each set of images I suspect it would be hard to reproduce sensible? results.? ? ?
Re: [ccp4bb] images
Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... phx Gerard Bricogne wrote: Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
Re: [ccp4bb] images
Perhaps we could use Poincare's argument(?), that knowing one cross section of the universe in all of its detail would allow forward and back-calculation of all previous states. Then the universe would be its own lab notebook/ archive, and we would not need to bother with all of these technicalities in the first place. The images, then, could be back-calculated from the current (or any) configuration of all the universe's atoms, and then we could work better on improving our crystallography software (and ferreting out fraud) from those... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Frank von Delft frank.vonde...@sgc.ox.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 1:19 PM Subject: Re: [ccp4bb] images Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... phx Gerard Bricogne wrote: Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
Re: [ccp4bb] images
May be wwPDB should introduce a clause that all structure depositions (upon release) must allow raw images accessible to anyone upon request provided the requester pays (for postage and/or CD/DVD - if applicable). This may be followed until google/NSA will offer free and _reliable_ storage in a neighbouring planet forever. AFAIK, GPL based software agreements work like this. Karthik Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
Re: [ccp4bb] images
expressing, purifying and crystalizing the protein They are also useful. The NIH PSI initiative for example is trying as a part of their Protein Structure Knowledgebase to establish a material repository. How well this will be generally accepted is another question, and the storage and retrieval problem is even more formidable than the comparatively simple storage of images. http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=37 The time for such material and data repositories certainly has come. But even simple tasks such as analyzing and data-mining all crystallization data from all centers are still not readily possible. Others and myself pointed this out over the years in various publications - for example emphasizing consistent metrics etc etc, but not much has changed. It is an enormous loss of opportunity for information gain, just as neglecting diffraction images. The issue of standardization is in most situations a very difficult one. Just see the multitude of opinions on the ccp4bb. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Liz Potterton Sent: Wednesday, March 18, 2009 10:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear CCP4BB, For further research of a particular structure wouldn't hints on expressing, purifying and crystalizing the protein often be more useful than images or amplitudes? Liz
Re: [ccp4bb] images
Hi, Since my mailbox is swimming in 'Images!' emails I would add my irrelevant two cents: Image storage does not pay for itself. There has to be a source of funding for it. Storing, transmitting, etc. of the ever-increasing number of terabytes costs money, which at the moment no one seems to have [if you do, please say so - I am sure that large numbers of very smart (but financially disadvantaged) people are available to design a very nice system for image storage, if only there was some way to pay for it]. In my opinion all other arguments are very elegant and probably most of them are correct - but ultimately pointless until someone figures out a way to get the cash for this enterprise. Monstra mihi pecuniam! Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: Wednesday, March 18, 2009 3:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images expressing, purifying and crystalizing the protein They are also useful. The NIH PSI initiative for example is trying as a part of their Protein Structure Knowledgebase to establish a material repository. How well this will be generally accepted is another question, and the storage and retrieval problem is even more formidable than the comparatively simple storage of images. http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=37 The time for such material and data repositories certainly has come. But even simple tasks such as analyzing and data-mining all crystallization data from all centers are still not readily possible. Others and myself pointed this out over the years in various publications - for example emphasizing consistent metrics etc etc, but not much has changed. It is an enormous loss of opportunity for information gain, just as neglecting diffraction images. The issue of standardization is in most situations a very difficult one. Just see the multitude of opinions on the ccp4bb. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Liz Potterton Sent: Wednesday, March 18, 2009 10:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear CCP4BB, For further research of a particular structure wouldn't hints on expressing, purifying and crystalizing the protein often be more useful than images or amplitudes? Liz
Re: [ccp4bb] images
Dear Bernhard, Re-reading your previous message, I can see that I did indeed misread it, and I apologise for that. Perhaps it was the expression put to rest in relation to a topic where so much action is needed that made me charge in the wrong direction. Although this thread is now attracting additional suggestions about what else it might be a good thing to archive, this should not result in a dilution of the urgency of this particular item. As for the argument that any new task can only be done if there is extra money, then isn't this the ideal time to argue that we need a PDB stimulus package? After all, the PDB is a bank ... . With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 12:14:29PM -0700, Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] images
All right: How about then putting in a NIH challenge grant (due April 27) for image archiving? Who is in? BR -Original Message- From: Gerard Bricogne [mailto:g...@globalphasing.com] Sent: Wednesday, March 18, 2009 4:12 PM To: Bernhard Rupp Cc: 'Gerard Bricogne'; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, Re-reading your previous message, I can see that I did indeed misread it, and I apologise for that. Perhaps it was the expression put to rest in relation to a topic where so much action is needed that made me charge in the wrong direction. Although this thread is now attracting additional suggestions about what else it might be a good thing to archive, this should not result in a dilution of the urgency of this particular item. As for the argument that any new task can only be done if there is extra money, then isn't this the ideal time to argue that we need a PDB stimulus package? After all, the PDB is a bank ... . With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 12:14:29PM -0700, Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] images
Some of us have already been discussing that possibility. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Bernhard Rupp wrote: All right: How about then putting in a NIH challenge grant (due April 27) for image archiving? Who is in? BR -Original Message- From: Gerard Bricogne [mailto:g...@globalphasing.com] Sent: Wednesday, March 18, 2009 4:12 PM To: Bernhard Rupp Cc: 'Gerard Bricogne'; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, Re-reading your previous message, I can see that I did indeed misread it, and I apologise for that. Perhaps it was the expression put to rest in relation to a topic where so much action is needed that made me charge in the wrong direction. Although this thread is now attracting additional suggestions about what else it might be a good thing to archive, this should not result in a dilution of the urgency of this particular item. As for the argument that any new task can only be done if there is extra money, then isn't this the ideal time to argue that we need a PDB stimulus package? After all, the PDB is a bank ... . With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 12:14:29PM -0700, Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] images
The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. The research council policy in the UK is that original data is meant to be archived for publicly funded projects. Maybe someone should test the reality of this by asking the PI for the data sets? Eleanor Garib Murshudov wrote: Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs observed statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for mistakes. They are doing their best to produce and deposit. There should be a proper mechanism to reduce the number of mistakes. You should agree that situation is now much better than few years. 2) A fundamental problem: What are observed data? I agree with you (Gerard) that images are only true observations. All others (intensities, amplitudes etc) have undergone some processing using some assumptions and they cannot be considered as true observations. The dataprocessing is irreversible process. I hope your effort will be supported by community. I personally get excited with the idea that images may be available. There are exciting possibilities. For example modular crystals, OD, twin in general, space group uncertaintly cannot be truly modeled without images (it does not mean refinement against images). Radiation damage is another example where after processing and merging information is lost and cannot be recovered fully. You can extend the list where images would be very helpful. I do not know any reason (apart from technical one - size of files) why images should not be deposited and archived. I think this problem is very important. regards Garib On 12 Mar 2009, at 14:03, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] images
Hi I'm afraid the adoption of imgCIF (or CBF, its useful binary equivalent) doesn't help a lot - I know of three different manufacturers of detectors who, between them, write out four different image formats, all of which apparently conform to the agreed IUCr imgCIF standard. Each manufacturer has its own good and valid reasons for doing this. It's actually less work for me as a developer of integration software to write new code to incorporate a new format than to make sure I can read all the different imgCIFs properly. On 16 Mar 2009, at 09:32, Eleanor Dodson wrote: The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. The research council policy in the UK is that original data is meant to be archived for publicly funded projects. Maybe someone should test the reality of this by asking the PI for the data sets? Eleanor Garib Murshudov wrote: Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/ sigma, some statistical analysis expected vs observed statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for mistakes. They are doing their best to produce and deposit. There should be a proper mechanism to reduce the number of mistakes. You should agree that situation is now much better than few years. 2) A fundamental problem: What are observed data? I agree with you (Gerard) that images are only true observations. All others (intensities, amplitudes etc) have undergone some processing using some assumptions and they cannot be considered as true observations. The dataprocessing is irreversible process. I hope your effort will be supported by community. I personally get excited with the idea that images may be available. There are exciting possibilities. For example modular crystals, OD, twin in general, space group uncertaintly cannot be truly modeled without images (it does not mean refinement against images). Radiation damage is another example where after processing and merging information is lost and cannot be recovered fully. You can extend the list where images would be very helpful. I do not know any reason (apart from technical one - size of files) why images should not be deposited and archived. I think this problem is very important. regards Garib On 12 Mar 2009, at 14:03, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/ sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * 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 * * * === Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] images
Dear Colleagues, The issue Harry is describing, of people writing multiple variations of image formats even though all of them are imgCIF is not really a problems with the images themselves. Rather it is a lack of agreement on the metadata to go with the images. This is similar to the problem of lack of consistency in REMARKS for early PDB data sets, which eventually required the adoption of standardized REMARKS and reprocessing of almost all data sets. I don't think it would have been easier to reprocess those data sets if the original data sets had also had their coordinates and sequences recorded with wide variations in formats. The advantage of using imgCIF for an archive is not that it would force everybody to to their experiments using precisely the same format, but that, because it is capable of faithfully representing all the wide variations in current formats, it would allow what we now have to be captured and preserved and, when someone needed a dataset back, to be recast in an format appropriate to the use. Think of it as that little figure-8 plug and socket we are able to use to adapt our power cords for travel around the world. There are other possible hub format (NeXus, DICOM, etc.), but the sensisble thing for an archive is to choose one of them for internal use, just as the PDB uses a variation on mmCIF for its internal use to allow it to easily deliver valid PDB, CIF and XML versions of sets of coordinates. For an archive, the advantages of using imgCIF internally, no matter which of the more than 200 current formats were to be used at beam lines and in labs, is that it would not be necessary to discard any of the metadata people provided and it could be made to interoperate easily with the systems used internally by the PDB for coordinate data sets. For many of the formats in current use, there is no place to store some of the information people provide and translation to other formats can sometimes be much more difficult than one might expect unless additional metadata is provided. Even such obvious things as image orientations are sometimes carried separately from the images themselves and can easily get lost. Don't let the perfect be the enemy of the good. Archiving images in a common format, such as imgCIF, or, if you prefer, say, in the NeXus transliteration of imgCIF, would help to make some very useful information accessible for future use. It may not be a perfect solution, but it is a good one. This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? Regards, Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Mon, 16 Mar 2009, Harry Powell wrote: Hi I'm afraid the adoption of imgCIF (or CBF, its useful binary equivalent) doesn't help a lot - I know of three different manufacturers of detectors who, between them, write out four different image formats, all of which apparently conform to the agreed IUCr imgCIF standard. Each manufacturer has its own good and valid reasons for doing this. It's actually less work for me as a developer of integration software to write new code to incorporate a new format than to make sure I can read all the different imgCIFs properly. On 16 Mar 2009, at 09:32, Eleanor Dodson wrote: The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. The research council policy in the UK is that original data is meant to be archived for publicly funded projects. Maybe someone should test the reality of this by asking the PI for the data sets? Eleanor Garib Murshudov wrote: Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs observed statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for
[ccp4bb] images
Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs observed statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for mistakes. They are doing their best to produce and deposit. There should be a proper mechanism to reduce the number of mistakes. You should agree that situation is now much better than few years. 2) A fundamental problem: What are observed data? I agree with you (Gerard) that images are only true observations. All others (intensities, amplitudes etc) have undergone some processing using some assumptions and they cannot be considered as true observations. The dataprocessing is irreversible process. I hope your effort will be supported by community. I personally get excited with the idea that images may be available. There are exciting possibilities. For example modular crystals, OD, twin in general, space group uncertaintly cannot be truly modeled without images (it does not mean refinement against images). Radiation damage is another example where after processing and merging information is lost and cannot be recovered fully. You can extend the list where images would be very helpful. I do not know any reason (apart from technical one - size of files) why images should not be deposited and archived. I think this problem is very important. regards Garib On 12 Mar 2009, at 14:03, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/ sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * 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 * * * ===
