[ccp4bb] Postdoctoral Positions for collaborative DIAMOND Light Source / Synchrotron - SOLEIL Initiative
Dear All, We’d like to draw your attention to three PDRA posts (two at Diamond Light Source and one at Soleil) forming part of a collaborative initiative between Diamond Light Source in Didcot, UK and the Soleil synchrotron in Gif sur Yvette, France to develop methodology and automated analysis pipelines for synchrotron macromolecular crystallography: They are Diamond Light Source • Postdoctoral Researcher in Experimental Phasing Analysis for macromolecular crystallography (http://diamond.ac.uk/Home/Jobs/Current/DIA0786_CB.html) • Postdoctoral Researcher in Multicrystal X-ray Data Analysis for macromolecular crystallography (http://diamond.ac.uk/Home/Jobs/Current/DIA0785_CB.html) Soleil • Postdoctoral Researcher in Scaling methods and analysis for macromolecular crystallography (http://www.synchrotron-soleil.fr/images/File/soleil/DivisionAdministration/Personnel/2012/SOLEIL_postDoc_PROXIMA%201_2013.pdf ) All three researchers will work closely with beamline scientists and existing software developers at Diamond and Soleil to deliver integrated, expert system pipelines to assist beamline users in the measurement and analysis of diffraction data with a view to providing interpreted electron density at the beamline in minutes. Gwyndaf Evans and Andrew Thompson
[ccp4bb] NCS from electron density
Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas
Re: [ccp4bb] NCS from electron density
Hi, The only tool I'm aware of is Tom Terwiliger's phenix.find_ncs_from_density, the operators from which can be passed onto his phenix.ncs_average program. Most programs expect you to have heavy atom sites or protein models from which the NCS can be deduced. Regards, Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 12 Dec 2012, at 18:01, Nicolas Soler wrote: Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas
Re: [ccp4bb] NCS from electron density
I've had good experience with GETAX if you have a self rotation peak. Be careful about moving the NCS operator from program to program. Phenix/DM/RAVE all have specific formats for how it should be presented. F On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote: Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder
Re: [ccp4bb] NCS from electron density
Hi Francis, Do you have a specific how to on your experience with NCS (reference)? Cheers, Scott Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swals...@umd.edumailto:swals...@umd.edu On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote: I've had good experience with GETAX if you have a self rotation peak. Be careful about moving the NCS operator from program to program. Phenix/DM/RAVE all have specific formats for how it should be presented. F On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote: Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder
Re: [ccp4bb] NCS from electron density
Each case is specific, but when I was learning, I found Phil's Notes on Averaging (http://xray0.princeton.edu/~phil/Facility/averaging.html) to be quite useful. F On Dec 12, 2012, at 11:59 AM, Scott Thomas Walsh wrote: Hi Francis, Do you have a specific how to on your experience with NCS (reference)? Cheers, Scott Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swals...@umd.edu On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote: I've had good experience with GETAX if you have a self rotation peak. Be careful about moving the NCS operator from program to program. Phenix/DM/RAVE all have specific formats for how it should be presented. F On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote: Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder
[ccp4bb] archival memory?
SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
[ccp4bb] cysteine modification ??
Dear Users, I am currently refining a structure of a bacterial oxido-reductase enzyme and Im trying to fit extra density seen on a cysteine residue. Would appreciate some recommendations re. what this may be (here is a link to the map- http://sdrv.ms/XTNTFs ). There is clearly one extra atom here (seen in both chains very clearly), but unsure what it could be methylation? -SOH? The cysteine residue is not in the active site and is solvent exposed. The protein sequence was confirmed. Thanks for any help. Kirk Hevener ps: the map was contoured at 1.2sigma and the difference map at 3sigma
Re: [ccp4bb] archival memory?
Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] cysteine modification ??
Kirk, This is almost certainly S-hydroxycysteine. If the distance to the center of the density to the S-atom is about 1.6 A, that would be additional supporting information for an S-O bond. Under oxidizing conditions (exposure to air) it is possible for cysteines to become oxidized to the sulfenate. A recent structure of ours (3UAO) has a cysteine sulfenate in the active site which is almost certainly an artifact of storage in the absence of reducing agents. When we solve the structure of the enzyme from protein that has been protected from oxygen, this feature is not present and a normal Cys residue is observed. 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 On 12/12/2012 4:23 PM, Shahila Mehboob wrote: Dear Users, I am currently refining a structure of a bacterial oxido-reductase enzyme and I’m trying to fit extra density seen on a cysteine residue. Would appreciate some recommendations re. what this may be (here is a link to the map- http://sdrv.ms/XTNTFs ). There is clearly one extra atom here (seen in both chains very clearly), but unsure what it could be … methylation? -SOH? The cysteine residue is not in the active site and is solvent exposed. The protein sequence was confirmed. Thanks for any help. Kirk Hevener ps: the map was contoured at 1.2sigma and the difference map at 3sigma
Re: [ccp4bb] archival memory?
Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
Ha ha. Brilliant! Maybe we should just send them up to Svalbard to store with the seeds. On Dec 12, 2012, at 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ 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 On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edu mailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
I don't think memory sticks have any internal electrolytics or power supplies. Both USB and FAT32 are widely documented standards in this era, so while they might no longer be supported (FAT32 is already very old), information on how to communicate and decode data will still likely be available. RS232, for example, is now 50 years old and one can still find adapters and software. Richard On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ 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.edumailto:rrowl...@colgate.edu On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
You know if you took a dremel to an insulated benchtop cold box to make USB shaped holes, lined the bottom with a layer of desiccant, and used a little vacuum grease to seal it up you might actually have a workable, long term, freezer storage system. Wow, the things you think up when you're avoiding grant writing. On Wed, Dec 12, 2012 at 3:45 PM, Roger Rowlett rrowl...@colgate.edu wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ 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 On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.eduwrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
I say write them out onto acid-free paper: should be good for at least 300 years without active management, if there is no fire. If that doesn't work, I believe babylonian clay tablets have an even longer expected life time…. Dale, I must say I am impressed… I gave up after the exabyte to DAT transition, and decided that if I really wanted to get data sets from (my) old projects, it would be easier to regrow the crystals… Adrian On 13 Dec 2012, at 00:22, Dale Tronrud wrote: I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
Given that it's basically a solid state tiny capacitor, temperature should indeed be a huge factor :) I am actually considering storing some flash sticks in a freezer, to see what happens. And in LN2 as well... Artem On Wed, Dec 12, 2012 at 4:14 PM, Richard Gillilan r...@cornell.edu wrote: I don't think memory sticks have any internal electrolytics or power supplies. Both USB and FAT32 are widely documented standards in this era, so while they might no longer be supported (FAT32 is already very old), information on how to communicate and decode data will still likely be available. RS232, for example, is now 50 years old and one can still find adapters and software. Richard On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ 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 On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.eduwrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
I would definitely go for babylonian clay... On Dec 12, 2012, at 10:31 PM, Adrian Goldman wrote: I say write them out onto acid-free paper: should be good for at least 300 years without active management, if there is no fire. If that doesn't work, I believe babylonian clay tablets have an even longer expected life time…. Dale, I must say I am impressed… I gave up after the exabyte to DAT transition, and decided that if I really wanted to get data sets from (my) old projects, it would be easier to regrow the crystals… Adrian On 13 Dec 2012, at 00:22, Dale Tronrud wrote: I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS Dr Laura Spagnolo Institute of Structural Molecular Biology University of Edinburgh Room 506, Darwin Building King's Buildings Campus Edinburgh EH9 3JR United Kingdom T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo laura.spagn...@ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Re: [ccp4bb] archival memory?
encoding into DNA and transforming some long lived critter is the best solution for me. My mind's eye is watering with glee when I imagine how TurtleBank might look -- fields of green grass, populated by herds of gentle grazing turtles, each encoding some priceless tidbit of information. Of course, worrying about access to USB formatted memory 100 years from now is likely not necessary. We should be able to read these chips directly using a miniaturized form of scanning microscopy or somesuch (probably non-invasive, unlike SEM). Charge-state of a floating gate transistor can be derived by e.g. a properly designed SEM tip right now (this is one of the methods used to steal data from protected flash drives by the way), but i am SURE that in a century the technology to read the state of matter should be advanced to a level of household implementation. Anyway. On Wed, Dec 12, 2012 at 4:35 PM, Artem Evdokimov artem.evdoki...@gmail.comwrote: Given that it's basically a solid state tiny capacitor, temperature should indeed be a huge factor :) I am actually considering storing some flash sticks in a freezer, to see what happens. And in LN2 as well... Artem On Wed, Dec 12, 2012 at 4:14 PM, Richard Gillilan r...@cornell.eduwrote: I don't think memory sticks have any internal electrolytics or power supplies. Both USB and FAT32 are widely documented standards in this era, so while they might no longer be supported (FAT32 is already very old), information on how to communicate and decode data will still likely be available. RS232, for example, is now 50 years old and one can still find adapters and software. Richard On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ 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 On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.eduwrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
A chip in my brain to remember all of the things I should know/remember would be very convenient if we are really talking about having a good memory system. It means it would also be easier to extract that personal perspective and pass it on. Cheers, tom From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Artem Evdokimov Sent: Thursday, 13 December 2012 9:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] archival memory? encoding into DNA and transforming some long lived critter is the best solution for me. My mind's eye is watering with glee when I imagine how TurtleBank might look -- fields of green grass, populated by herds of gentle grazing turtles, each encoding some priceless tidbit of information. Of course, worrying about access to USB formatted memory 100 years from now is likely not necessary. We should be able to read these chips directly using a miniaturized form of scanning microscopy or somesuch (probably non-invasive, unlike SEM). Charge-state of a floating gate transistor can be derived by e.g. a properly designed SEM tip right now (this is one of the methods used to steal data from protected flash drives by the way), but i am SURE that in a century the technology to read the state of matter should be advanced to a level of household implementation. Anyway. On Wed, Dec 12, 2012 at 4:35 PM, Artem Evdokimov artem.evdoki...@gmail.commailto:artem.evdoki...@gmail.com wrote: Given that it's basically a solid state tiny capacitor, temperature should indeed be a huge factor :) I am actually considering storing some flash sticks in a freezer, to see what happens. And in LN2 as well... Artem On Wed, Dec 12, 2012 at 4:14 PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: I don't think memory sticks have any internal electrolytics or power supplies. Both USB and FAT32 are widely documented standards in this era, so while they might no longer be supported (FAT32 is already very old), information on how to communicate and decode data will still likely be available. RS232, for example, is now 50 years old and one can still find adapters and software. Richard On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245tel:%28315%29-228-7245 ofc: (315)-228-7395tel:%28315%29-228-7395 fax: (315)-228-7935tel:%28315%29-228-7935 email: rrowl...@colgate.edumailto:rrowl...@colgate.edu On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS
Re: [ccp4bb] archival memory?
Punched cards, stored in a sealed dry box, and perhaps irradiated to kill off any bacteria, should long outlive any magnetic or capacitive storage medium. If it is difficult to find a working card reader, they could always be read by eye, though that might be tedious. Their EBCDIC code is not ASCII, but at least it is well documented. George On 12/12/2012 11:35 PM, Artem Evdokimov wrote: Given that it's basically a solid state tiny capacitor, temperature should indeed be a huge factor :) I am actually considering storing some flash sticks in a freezer, to see what happens. And in LN2 as well... Artem On Wed, Dec 12, 2012 at 4:14 PM, Richard Gillilan r...@cornell.edu mailto:r...@cornell.edu wrote: I don't think memory sticks have any internal electrolytics or power supplies. Both USB and FAT32 are widely documented standards in this era, so while they might no longer be supported (FAT32 is already very old), information on how to communicate and decode data will still likely be available. RS232, for example, is now 50 years old and one can still find adapters and software. Richard On Dec 12, 2012, at 4:45 PM, Roger Rowlett wrote: Maybe the memory chips will retain their bits for 100 years, but what about the driver hardware or internal power supply? Anyone had an electrolytic capacitor last for 100 years? Just sayin... I like the image of the USB sticks in the -80 freezer, though. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 tel:%28315%29-228-7245 ofc: (315)-228-7395 tel:%28315%29-228-7395 fax: (315)-228-7935 tel:%28315%29-228-7935 email: rrowl...@colgate.edu mailto:rrowl...@colgate.edu On 12/12/2012 4:38 PM, Artem Evdokimov wrote: Or... (gasp) store a regular USB drive in a freezer, yes? If the relationship between data decay rate and temperature indeed follows the same good old Arrhenius formula then any old USB drive is virtually endless at -80C and safe for human life span at -20 (i.e. kitchen freezer, sans defrost cycles (so pack your USB in some ice packs so defrost doesn't kill it). If this works, feel free to send me money, SanDisk... Artem On Wed, Dec 12, 2012 at 3:02 PM, Richard Gillilan r...@cornell.edu mailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] archival memory?
On 12/12/2012 3:19 PM, Bosch, Juergen wrote: Hey Dale, you really should get your personal RAID with hot swappable discs, since you don't like Firewire, how about Thunderbolt and a Pegasus RAID with 6 bays ? If a drive fails you replace it with a new one. Last summer someone in the lab above ours decided they needed a full sink of water. Before this task was complete they decided they needed to go home. The resulting flood destroyed the contents of the desks of two of our lab members. That was a lot of paper that didn't make 100 years - including a Handbook of Chemistry and Physics that had almost made 60. If the lab RAID had been under the waterfall it would have lost all of its drives in one go. I don't know how big a RAID number you have to have to survive that, but RAID-5 isn't going to do it. I have run a flash drive through my washing machine a couple times and it is still going strong so I have high hopes for solid-state memory. It will be several years before 1 TB SSD's drop in price enough for the next move of my little archive. The SanDisk Memory Vault that started this thread maxes out at 16 GB. Dale Tronrud By the way if anybody has a functional DAT4 tape drive, could I send you one to read out a tape with some data ? If so, then off list reply would be nice, thanks. Jürgen On Dec 12, 2012, at 5:22 PM, Dale Tronrud wrote: I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS .. 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://lupo.jhsph.edu
Re: [ccp4bb] archival memory?
Don't get your hopes up too high for ssd. I had one fail within 4 months of buying it - and the company's attitude was 'this sometimes happens'. Yum I think George is right - punched cards in two separate locations. (Hell any form of paper output will do - surely they'll have decent OCR in 100 years time)? Adrian Sent from my iPhone On 13 Dec 2012, at 02:32, Dale Tronrud det...@uoxray.uoregon.edu wrote: On 12/12/2012 3:19 PM, Bosch, Juergen wrote: Hey Dale, you really should get your personal RAID with hot swappable discs, since you don't like Firewire, how about Thunderbolt and a Pegasus RAID with 6 bays ? If a drive fails you replace it with a new one. Last summer someone in the lab above ours decided they needed a full sink of water. Before this task was complete they decided they needed to go home. The resulting flood destroyed the contents of the desks of two of our lab members. That was a lot of paper that didn't make 100 years - including a Handbook of Chemistry and Physics that had almost made 60. If the lab RAID had been under the waterfall it would have lost all of its drives in one go. I don't know how big a RAID number you have to have to survive that, but RAID-5 isn't going to do it. I have run a flash drive through my washing machine a couple times and it is still going strong so I have high hopes for solid-state memory. It will be several years before 1 TB SSD's drop in price enough for the next move of my little archive. The SanDisk Memory Vault that started this thread maxes out at 16 GB. Dale Tronrud By the way if anybody has a functional DAT4 tape drive, could I send you one to read out a tape with some data ? If so, then off list reply would be nice, thanks. Jürgen On Dec 12, 2012, at 5:22 PM, Dale Tronrud wrote: I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS .. 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://lupo.jhsph.edu
Re: [ccp4bb] archival memory?
On 13/12/2012 04:13, Adrian Goldman wrote: Don't get your hopes up too high for ssd. I had one fail within 4 months of buying it - and the company's attitude was 'this sometimes happens'. Yum I think George is right - punched cards in two separate locations. (Hell any form of paper output will do - surely they'll have decent OCR in 100 years time)? Awesome - punchcard RAID-1. Adrian Sent from my iPhone On 13 Dec 2012, at 02:32, Dale Tronrud det...@uoxray.uoregon.edu wrote: On 12/12/2012 3:19 PM, Bosch, Juergen wrote: Hey Dale, you really should get your personal RAID with hot swappable discs, since you don't like Firewire, how about Thunderbolt and a Pegasus RAID with 6 bays ? If a drive fails you replace it with a new one. Last summer someone in the lab above ours decided they needed a full sink of water. Before this task was complete they decided they needed to go home. The resulting flood destroyed the contents of the desks of two of our lab members. That was a lot of paper that didn't make 100 years - including a Handbook of Chemistry and Physics that had almost made 60. If the lab RAID had been under the waterfall it would have lost all of its drives in one go. I don't know how big a RAID number you have to have to survive that, but RAID-5 isn't going to do it. I have run a flash drive through my washing machine a couple times and it is still going strong so I have high hopes for solid-state memory. It will be several years before 1 TB SSD's drop in price enough for the next move of my little archive. The SanDisk Memory Vault that started this thread maxes out at 16 GB. Dale Tronrud By the way if anybody has a functional DAT4 tape drive, could I send you one to read out a tape with some data ? If so, then off list reply would be nice, thanks. Jürgen On Dec 12, 2012, at 5:22 PM, Dale Tronrud wrote: I don't believe there is a solution that does not involve active management. You can't write your data and pick up those media 25 years later and expect to get your data back -- not without some heroic effort involving the construction of your own hardware. I have data from Brian Matthews' lab going back to the mid-1970's and those data started life on 7-track mag tapes. I've moved them from there to 9-track 1600 bpi tapes, to 9-track 6250 bpi tapes, to just about every density of Exabyte tape, to DVD, and most recently to external magnetic hard drives (each with USB, Firewire, and eSATA interfaces). The hard drives are about five years old and so far are holding up. Last time I checked I could still read the 10 year old DVD's. I'm having real trouble reading Exabyte tapes. Write your data to some medium that you expect to last for at least five years but anticipate that you will then have to move them to something else. Instead of spending time working on the 100 year solution you should spend your time annotating your data so that someone other than you can figure out what it is. Lack of annotation and editing is the biggest problem with old data. Dale Tronrud P.S. If someone needs the intensities for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might be a cloud solution where you rely upon data just floating around out there in cyberspace with a life of its own. Richard On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out: www.sandisk.com/products/usb/memory-vault/ http://www.sandisk.com/products/usb/memory-vault/ and click the Chronolock tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS .. 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://lupo.jhsph.edu
Re: [ccp4bb] refining against weak data and Table I stats
I think CC* (derived from CC1/2) is an important step forward in how to decide where to cut off the data you give to your refinement program, but I don't think it is a good idea to re-define what we call the resolution of a structure. These do NOT have to be the same thing! Remember, what we crystallographers call resolution is actually about 3x the resolution a normal person would use. That is, for most types of imaging whether it be 2D (pictures of Mars) or 3D (such as electron density) the resolution is the minimum feature size you can reliably detect in the image. This definition of resolution makes intuitive sense, especially to non-crystallographers. It is also considerably less pessimistic than our current definition since the minimum observable feature size in an electron density map is about 1/3 of the d-spacing of the highest-angle spots. This is basically because the d-spacing is the period of a sine wave in space, but the minimum feature size is related to the full-width at half max of this same wave. So, all you have to do is change your definition of resolution and a 3.0 A structure becomes a 1.0 A structure! However, I think proposing this new way to define resolution in crystallography will be met with some resistance. Why? Because changing the meaning of resolution so drastically after ~100 years would be devastating to its usefulness in structure evaluation. I, for one, do not want to have to check the deposition date and see if the structure was solved before or after the end of the world (Dec 2012) before I can figure out whether or not I need to divide or multiply by 3 to get the real resolution of the structure. I don't think I'm alone in this. Now, calling what used to be a 1.6 A structure a 1.42 A structure (one way to interpret Karplus Diederichs 2012) is not quite as drastic a change as the one I flippantly propose above, but it is still a change, and there is a real danger of definition creep here. Most people these days seem to define the resolution limit of their data at the point where the merged I/sigma(I) drops below 2. However, using CC* = 0.5 would place the new resolution at the point where merged I/sigma(I) drops below 0.5. That's definitely going beyond what anyone would have called the resolution of the structure last year. So, which one is it? Is it a 1.6 A structure (refined using data out to 1.42 A), or is it actually a 1.42 A structure? Unfortunately, if you talk to a number of experienced crystallographers, they will each have a slightly different set of rules for defining the resolution limit that they learned from their thesis advisor, who, in turn, learned it from theirs, etc. Nearly all of these rule sets include some reference to Rmerge, but the acceptable Rmerge seems to vary from 30% to as much as 150%, depending on whom you talk to. However, despite this prevalence of Rmerge in our perception of resolution there does not seem to be a single publication anywhere in the literature that recommends the use of Rmerge to define the resolution limit. Several papers have been cited to that effect, but then if you go and read them they actually made no such claim. Mathematically, it is fairly easy to show that Rmerge is wildly unstable as the average intensity approaches zero, so how did we get stuck on it as a criterion for evaluating the outer resolution bin? I'm not really sure, but I think it must have happened around 1995. Before that, there are NO entries for Rmerge in the high-resolution bin in the PDB. Not one. Looking at papers from the pre-1995 era, you don't see it reported in table 1 either. What is more, ever since 1995, the average reported Rmerge in the high-resolution shell has been slowly rising by about 1.6 percentage points each year. Started around 20%, and now it is up to 50%. Seriously. Here is the graph: http://bl831.als.lbl.gov/~jamesh/pickup/outershell_Rmerge.png I think this could be yet another example of definition creep. For any given year, I imagine a high-resolution Rmerge that is only a few percent worse than the average over the PDB at that time is probably considered okay, and the average just keeps increasing over time. Nevertheless, Rmerge is a useful statistic for evaluating the quality of a diffractometer, provided it is used in the way it was originally defined by Uli Arndt: over the entire dataset for spots with I/sd 3. At large multiplicity, the Rmerge calculated this way asymptotically approaches the average % error for measuring a single spot. If it is more than 5% or so, then there might be something wrong with the camera (or the space group choice, etc). This is only true for Rmerge of ALL the data, not when it is relegated to a given resolution bin. Perhaps it is time we did have a discussion about what we mean by the resolution of a structure so that some kind of historically relevant and future proof
Re: [ccp4bb] refining against weak data and Table I stats
I like the R1 idea... report CC* and R1. Of course, anisotropy screws up everything (what do our small molecule friends know about that - ha!). So earlier in the thread, Ed Berry brought up the effective resolution: Bart Hazes (I think) suggested a statistic called effective resolution which is the resolution to which a complete dataset would have the number of reflections in your dataset. We just have to settle on how to determine number of reflections - maybe those with I/s 3? phx On 13/12/2012 06:52, James Holton wrote: I think CC* (derived from CC1/2) is an important step forward in how to decide where to cut off the data you give to your refinement program, but I don't think it is a good idea to re-define what we call the resolution of a structure. These do NOT have to be the same thing! Remember, what we crystallographers call resolution is actually about 3x the resolution a normal person would use. That is, for most types of imaging whether it be 2D (pictures of Mars) or 3D (such as electron density) the resolution is the minimum feature size you can reliably detect in the image. This definition of resolution makes intuitive sense, especially to non-crystallographers. It is also considerably less pessimistic than our current definition since the minimum observable feature size in an electron density map is about 1/3 of the d-spacing of the highest-angle spots. This is basically because the d-spacing is the period of a sine wave in space, but the minimum feature size is related to the full-width at half max of this same wave. So, all you have to do is change your definition of resolution and a 3.0 A structure becomes a 1.0 A structure! However, I think proposing this new way to define resolution in crystallography will be met with some resistance. Why? Because changing the meaning of resolution so drastically after ~100 years would be devastating to its usefulness in structure evaluation. I, for one, do not want to have to check the deposition date and see if the structure was solved before or after the end of the world (Dec 2012) before I can figure out whether or not I need to divide or multiply by 3 to get the real resolution of the structure. I don't think I'm alone in this. Now, calling what used to be a 1.6 A structure a 1.42 A structure (one way to interpret Karplus Diederichs 2012) is not quite as drastic a change as the one I flippantly propose above, but it is still a change, and there is a real danger of definition creep here. Most people these days seem to define the resolution limit of their data at the point where the merged I/sigma(I) drops below 2. However, using CC* = 0.5 would place the new resolution at the point where merged I/sigma(I) drops below 0.5. That's definitely going beyond what anyone would have called the resolution of the structure last year. So, which one is it? Is it a 1.6 A structure (refined using data out to 1.42 A), or is it actually a 1.42 A structure? Unfortunately, if you talk to a number of experienced crystallographers, they will each have a slightly different set of rules for defining the resolution limit that they learned from their thesis advisor, who, in turn, learned it from theirs, etc. Nearly all of these rule sets include some reference to Rmerge, but the acceptable Rmerge seems to vary from 30% to as much as 150%, depending on whom you talk to. However, despite this prevalence of Rmerge in our perception of resolution there does not seem to be a single publication anywhere in the literature that recommends the use of Rmerge to define the resolution limit. Several papers have been cited to that effect, but then if you go and read them they actually made no such claim. Mathematically, it is fairly easy to show that Rmerge is wildly unstable as the average intensity approaches zero, so how did we get stuck on it as a criterion for evaluating the outer resolution bin? I'm not really sure, but I think it must have happened around 1995. Before that, there are NO entries for Rmerge in the high-resolution bin in the PDB. Not one. Looking at papers from the pre-1995 era, you don't see it reported in table 1 either. What is more, ever since 1995, the average reported Rmerge in the high-resolution shell has been slowly rising by about 1.6 percentage points each year. Started around 20%, and now it is up to 50%. Seriously. Here is the graph: http://bl831.als.lbl.gov/~jamesh/pickup/outershell_Rmerge.png I think this could be yet another example of definition creep. For any given year, I imagine a high-resolution Rmerge that is only a few percent worse than the average over the PDB at that time is probably considered okay, and the average just keeps increasing over time. Nevertheless, Rmerge is a useful statistic for evaluating the quality of a diffractometer, provided it is used in the way it was originally defined by Uli Arndt: over the
