Re: [ccp4bb] vitrification vs freezing
Dear Andrew, Re cryocooled. Cooled? It reminds me of James Bond where Martinis should be shaken but not stirred. Ie Cooling sounds awfully gentle, a sort of enjoying a cool sea breeze in the Caribbean heat. (Ian Fleming wrote his Bond novels there.) Shock frozen is more what we are doing to our crystals, a brutal event, rather than a cooling, even if labelled cryo cooling. Greetings, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html On 15 Nov 2012, at 18:12, A Leslie wrote: > Dear Sebastiano, > >This is not entirely straight-forward. The > Oxford English dictionary gives the first definition of "freeze" relevant to > this discussion as: > "Of (a body of) water: be converted into or become covered with ice through > loss of heat" > > This is certainly not what we want to do to our crystals. > > However, another definition in OED is: > "Cause (a liquid) to solidify by removal of heat", suggesting that this does > not necessarily mean the formation of crystals. > > The Larousse Dictionary of Science and Technology (1995) has the following > definition: > "Freeze-drying (Biol.) A method of fixing tissues sufficiently rapidly as to > inhibit the formation of ice-crystals." > > The Dictionary of Microbiology and Molecular Biology (3rd Ed) in the entry on > "Freezing" has the sentence: > "Rapid freezing tends to prevent the ice crystal formation by encouraging > vitrification". > > Both of these erstwhile volumes therefore suggest that freezing does not > necessarily imply the formation of crystals. However, the term is ambiguous, > while vitrification is not. > > Personally I use "cryocooled" instead. > > Best wishes, > > Andrew > > > > On 15 Nov 2012, at 17:13, Sebastiano Pasqualato wrote: > >> >> Hi folks, >> I have recently received a comment on a paper, in which referee #1 >> (excellent referee, btw!) commented like this: >> >> "crystals were vitrified rather than frozen." >> >> These were crystals grew in ca. 2.5 M sodium malonate, directly dip in >> liquid nitrogen prior to data collection at 100 K. >> We stated in the methods section that crystals were "frozen in liquid >> nitrogen", as I always did. >> >> After a little googling it looks like I've always been wrong, and what we >> are always doing is doing is actually vitrifying the crystals. >> Should I always use this statement, from now on, or are there >> english/physics subtleties that I'm not grasping? >> >> Thanks a lot, >> ciao, >> s >> >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> >> please note the change in email address! >> sebastiano.pasqual...@ieo.eu >> >> >> >> >> >> >> >
Re: [ccp4bb] vitrification vs freezing
On 11/16/12 17:33, Adrian Goldman wrote: Bernard Dixon is merely copying the great essay by George Orwell 'politics and the english language'. Its well worth a read. In it, Orwell lays out about six simple rules for writing good english prose. Three of them are: never use the passive voice. ... Translating into science-speak: The passive voice should never be used. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] vitrification vs freezing
Bernard Dixon is merely copying the great essay by George Orwell 'politics and the english language'. Its well worth a read. In it, Orwell lays out about six simple rules for writing good english prose. Three of them are: never use the passive voice. Always use the anglosaxon word instead of the Latin one: Break any of the rules above rather than say something outright barbarous. Ie. I froze the crystals. Not the crystals were vitrified. Other languages have different rules - habits - for what makes for clarity of thought in prose. I think anyone who uses vitrified should ask themselves 'why I trying to write a simple idea in a way that a layman can't understand'? Just thought some short chain liquid hydrocarbon should be ejected in a parabolic arc under the force of gravity (g=9.81 m/s/s, ie the current planet at h=0 above mean sea level) in the direction of an inflammatory ongoing situation. Adrian Sent from my iPhone On 16 Nov 2012, at 21:01, Ed Pozharski wrote: > On 11/16/2012 12:54 PM, Kendall Nettles wrote: > >> I wouldn't go into the lab and say "did you cryo-cool those crystals yet?" >> or "check out this nice crystal. Its ready for vitrification". > > If we speak the way scientific articles are written... > > By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an > imaginary conversation at breakfast: > > "Daddy, I want cornflakes this morning. Must I have porridge?" > > "Yes. It has been suggested by mummy that, in view of the external coldness, > the eating of porridge by you will cause an increase in bodily temperature. > Furthermore, in regard to the already-mentioned temperature considerations, > your grandma-knitted gloves and wool-lining-hooded coat will have to be worn." > > "May I have some sugar on my porridge?" > > "The absence of sugar in the relevant bowl has been noted by daddy at an > earlier moment. However, further supplies of this substance are now being > brought by mummy from the appropriate vessel that is present in the kitchen." > > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? >Julian, King of Lemurs
Re: [ccp4bb] vitrification vs freezing
warning - tangential: Steven Pinker's talk/promo on his new-new book "The Sense of Style : Scientific Communication for the 21st Century" : * * http://video.mit.edu/watch/communicating-science-and-technology-in-the-21st-century-steven-pinker-12644/ -Bryan
Re: [ccp4bb] vitrification vs freezing
Hi Ed, > If we speak the way scientific articles are written... > > By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an > imaginary conversation at breakfast: > > "Daddy, I want cornflakes this morning. Must I have porridge?" > > "Yes. It has been suggested by mummy that, in view of the external coldness, > the eating of porridge by you will cause an increase in bodily temperature. > Furthermore, in regard to the already-mentioned temperature considerations, > your grandma-knitted gloves and wool-lining-hooded coat will have to be worn." Translating into common language: "Yes. It's cold outside, having porridge will keep you warmer and please wear your gloves and wool coat." > > "May I have some sugar on my porridge?" > > "The absence of sugar in the relevant bowl has been noted by daddy at an > earlier moment. However, further supplies of this substance are now being > brought by mummy from the appropriate vessel that is present in the kitchen." > Translating into common language: "The sugar bowl was empty, but mommy had replenished it." If scientific articles are written as long winded and ambiguous as above examples, which could be easily made more concise and less ambiguous in common language (as suggested above), then I favor reporting scientific findings using common language. BTW, Ed, I have been hoping that F1 would return to Indy so that you guys would come to visit ;) Quyen > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? >Julian, King of Lemurs
Re: [ccp4bb] vitrification vs freezing
In the 1975 paper, they describe taking crystals to -100C, but it wasn't done in a "flash" sort of way. They equilibrated the crystals with various solvent combinations as the temperature was reduced. Trying to recollect what was discussed by my lab mates nearly 40 years ago, I think the fact that the crystals were mounted in capillaries caused difficulties with plunging the crystals into liquid N2. We never tried it, but the thought of what would happen to the glass, etc was enough to keep us from doing the experiment. I think the reason it took years before people started routine flash cooling of crystals was because it was expensive and hard to do. You needed to buy a crystal cooling device, and you had to invest the time and energy in developing cryo-solutions. People were more excited about seeing the next interesting structure, and room temperature experiments were good enough for that. Ron On Fri, 16 Nov 2012, Gerard Bricogne wrote: Dear Quyen and Ron, Thank you for bringing up this work. I can remember hearing Greg Petsko give a seminar at the LMB in Cambridge around 1974, but I never read that paper. The seminar was about cooling crystals at 4C, and also about work done with Pierre Douzou to try and retain the high dielectric constant of water (e.g. with DMSO) when cooling hydrated crystals to temperatures well below the normal freezing point of water. This had to be done progressively, with successive increases in the concentration of DMSO, and without ever giving rise to a transition to a solid phase of the solvent; so it would seem to have lacked the "flash" component of today's methods. It may well be that their work went further into crystal cryo-cooling and vitrification, and that this extension was described in the JMB paper you quote but not yet in the version of his seminar that I heard. If so, thank you for pointing out this reference - but then, why wasn't it taken up earlier? With best wishes, Gerard. -- On Fri, Nov 16, 2012 at 01:37:58PM -0500, Quyen Hoang wrote: I was going to mention that too, but since I was a postdoc of Petsko my words could have been viewed as biased. Quyen On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp wrote: I'm a little confused. Petsko and others were doing low-temperature/freezing/vitrification crystal experiments in the 1970s, right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between what they were doing and what's done now. Ron On Fri, 16 Nov 2012, Gerard Bricogne wrote: Dear all, I think we are perhaps being a little bit insular, or blinkered, in this discussion. The breakthrough we are talking about, and don't know how to call, first occurred not in crystallography but in electron microscopy, in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see for instance http://www.unil.ch/dee/page53292.html). It made possible the direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve higher resolution than the previous technique of negative staining. In that context it is obvious that the vitreous state refers to water, not to the macromolecular species embedded in it: the risk of a potential oxymoron in the crystallographic case arises from trying to choose a single adjective to qualify a two-component sample in which those components behave differently under sudden cooling. I have always found that an expression like "flash-frozen" has a lot going for it: it means that the sample was cooled very quickly, so it describes a process rather than a final state. The fact that this final state preserves the crystalline arrangement of the macromolecule(s), but causes the solvent to go into a vitreous phase, is just part of what every competent reviewer of a crystallographic paper should know, and that ought to avoid the kind of arguments that started this thread. With best wishes, Gerard. -- On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: Hi Sebastiano, I think the term "vitrified crystal" could be understood as a very nice oxymoron (http://www.oxymoronlist.com/), but it is essentially self-contradictory and not technically correct. As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a disordered solid state by definition, then it can't be a crystal. A vitrified crystal would be a crystal which has lost all three-dimensional ordering, pretty much like the material one gets when using the wrong "cryo-protectant". What one usually does is to soak the crystal in a "cryo-protectant" and then flash-freeze the resulting material, hoping that the crystal structure will be preserved, while the rest remains disordered in a solid state (vitrified), so that it won't produce a diffraction pattern by itself, and will hold the crystal in a fixed position (very convenient for data collection). Moreover, I would say that clarifying a material is vitrified when subjected to liquid N2 temperatures wo
Re: [ccp4bb] vitrification vs freezing
On Nov 16, 2012, at 12:01 PM, Ed Pozharski wrote: > On 11/16/2012 12:54 PM, Kendall Nettles wrote: > >> I wouldn't go into the lab and say "did you cryo-cool those crystals yet?" >> or "check out this nice crystal. Its ready for vitrification". >> > > If we speak the way scientific articles are written... > > By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an > imaginary conversation at breakfast: > > "Daddy, I want cornflakes this morning. Must I have porridge?" > > "Yes. It has been suggested by mummy that, in view of the external coldness, > the eating of porridge by you will cause an increase in bodily temperature. > Furthermore, in regard to the already-mentioned temperature considerations, > your grandma-knitted gloves and wool-lining-hooded coat will have to be worn." The imprecision of this language is staggering. For instance, the meaning of the word "worn" is completely ambiguous and should be clarified. Does the author mean that the coat (what kind?) should be draped over the child's head, tied around the child's waste, or should his arms be placed through the sleeves. If the latter, should the fasteners (what kind?) be dorsal or ventral? James
Re: [ccp4bb] vitrification vs freezing
Actually, to echo Ron, many low-temperature/freezing/vitrification crystal experiments were done in the 1970's, some by Tsernoglou and Petsko, when they were both at Wayne State, I believe. However, the direction Jacques Dubochet was looking at was an extension of work from the early 1960's. EM researchers were looking at freezing of tissues for freeze-fracture imaging. They have tomes about freezing and the different zones of ice crystal formation and vitrification. In fact to bring it full circle, these electron microscopists cite Kathleen Lonsdale (of the International Tables fame) and here work on ice crystal diffraction in the 1950's. While I was trying to stay out of this discussion, I am in favor of "flash-freezing" or "flash-cooling" and have no problem with the word frozen to describe a crystal in liquid N2, regardless of the crystallinity (or lack thereof) of the ice. This is the exact opinion of the electron microscopists doing freeze-fracture imaging for over 50 years: the tissue was frozen with a cryogen (e.g., freon), and you looked for the regions that were vitrified. My 2 cents. Cheers, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp wrote: > I'm a little confused. Petsko and others were doing > low-temperature/freezing/vitrification crystal experiments in the 1970s, > right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between > what they were doing and what's done now. > > Ron > > On Fri, 16 Nov 2012, Gerard Bricogne wrote: > >> Dear all, >> >>I think we are perhaps being a little bit insular, or blinkered, in >> this discussion. The breakthrough we are talking about, and don't know how >> to call, first occurred not in crystallography but in electron microscopy, >> in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see >> for instance http://www.unil.ch/dee/page53292.html). It made possible the >> direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve >> higher resolution than the previous technique of negative staining. In that >> context it is obvious that the vitreous state refers to water, not to the >> macromolecular species embedded in it: the risk of a potential oxymoron in >> the crystallographic case arises from trying to choose a single adjective to >> qualify a two-component sample in which those components behave differently >> under sudden cooling. >> >>I have always found that an expression like "flash-frozen" has a lot >> going for it: it means that the sample was cooled very quickly, so it >> describes a process rather than a final state. The fact that this final >> state preserves the crystalline arrangement of the macromolecule(s), but >> causes the solvent to go into a vitreous phase, is just part of what every >> competent reviewer of a crystallographic paper should know, and that ought >> to avoid the kind of arguments that started this thread. >> >> >>With best wishes, >> >> Gerard. >> >> -- >> On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: >>> Hi Sebastiano, >>> >>> I think the term "vitrified crystal" could be understood as a very nice >>> oxymoron (http://www.oxymoronlist.com/), but it is essentially >>> self-contradictory and not technically correct. >>> >>> As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a >>> disordered solid state by definition, then it can't be a crystal. A >>> vitrified crystal would be a crystal which has lost all three-dimensional >>> ordering, pretty much like the material one gets when using the wrong >>> "cryo-protectant". >>> >>> What one usually does is to soak the crystal in a "cryo-protectant" and >>> then flash-freeze the resulting material, hoping that the crystal structure >>> will be preserved, while the rest remains disordered in a solid state >>> (vitrified), so that it won't produce a diffraction pattern by itself, and >>> will hold the crystal in a fixed position (very convenient for data >>> collection). >>> >>> Moreover, I would say that clarifying a material is vitrified when >>> subjected to liquid N2 temperatures would be required only if you were >>> working with some liquid solvent which might remain in the liquid phase at >>> that temperature, instead of the usual solid disordered state, but this is >>> never the case with protein crystals. >>> >>> So, I vote for "frozen crystal".- >>> >>> Javier >>> >>> >>> PS: that comment by James Stroud "I forgot to mention that if any >>> dictionary is an authority on the very cold, it would be the Penguin >>> dic
Re: [ccp4bb] vitrification vs freezing
On 11/16/2012 12:54 PM, Kendall Nettles wrote: I wouldn't go into the lab and say "did you cryo-cool those crystals yet?" or "check out this nice crystal. Its ready for vitrification". If we speak the way scientific articles are written... By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an imaginary conversation at breakfast: "Daddy, I want cornflakes this morning. Must I have porridge?" "Yes. It has been suggested by mummy that, in view of the external coldness, the eating of porridge by you will cause an increase in bodily temperature. Furthermore, in regard to the already-mentioned temperature considerations, your grandma-knitted gloves and wool-lining-hooded coat will have to be worn." "May I have some sugar on my porridge?" "The absence of sugar in the relevant bowl has been noted by daddy at an earlier moment. However, further supplies of this substance are now being brought by mummy from the appropriate vessel that is present in the kitchen." -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] vitrification vs freezing
On Nov 16, 2012, at 12:26 PM, Ronald E Stenkamp wrote: > I'm a little confused. Petsko and others were doing > low-temperature/freezing/vitrification crystal experiments in the 1970s, > right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between > what they were doing and what's done now. > > Ron >From Greg's paper: "Since the mixed solvents used are fluid at low temperatures, diffusion of substrate into the crystals should be possible if the viscosity is not too high." One of his goals in the work reported in this paper was find fluid media that could be used at very low temperatures that would allow him to diffuse in substrates and trap a Michaelis complex and solve its structure. This is a bit different than the current "typical" cryopreservation practices that result in a solid system at or below 100K. It is noted that some increase in crystal lifetime is observed at the cold but not cryogenic temperatures explored in his work. Everyone will surely agree that he is one of the pioneers in collecting data on macromolecular crystals at low temperature.
Re: [ccp4bb] vitrification vs freezing
Dear Quyen and Ron, Thank you for bringing up this work. I can remember hearing Greg Petsko give a seminar at the LMB in Cambridge around 1974, but I never read that paper. The seminar was about cooling crystals at 4C, and also about work done with Pierre Douzou to try and retain the high dielectric constant of water (e.g. with DMSO) when cooling hydrated crystals to temperatures well below the normal freezing point of water. This had to be done progressively, with successive increases in the concentration of DMSO, and without ever giving rise to a transition to a solid phase of the solvent; so it would seem to have lacked the "flash" component of today's methods. It may well be that their work went further into crystal cryo-cooling and vitrification, and that this extension was described in the JMB paper you quote but not yet in the version of his seminar that I heard. If so, thank you for pointing out this reference - but then, why wasn't it taken up earlier? With best wishes, Gerard. -- On Fri, Nov 16, 2012 at 01:37:58PM -0500, Quyen Hoang wrote: > I was going to mention that too, but since I was a postdoc of Petsko my words > could have been viewed as biased. > > Quyen > > > > On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp > wrote: > > > I'm a little confused. Petsko and others were doing > > low-temperature/freezing/vitrification crystal experiments in the 1970s, > > right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference > > between what they were doing and what's done now. > > > > Ron > > > > On Fri, 16 Nov 2012, Gerard Bricogne wrote: > > > >> Dear all, > >> > >>I think we are perhaps being a little bit insular, or blinkered, in > >> this discussion. The breakthrough we are talking about, and don't know how > >> to call, first occurred not in crystallography but in electron microscopy, > >> in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see > >> for instance http://www.unil.ch/dee/page53292.html). It made possible the > >> direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve > >> higher resolution than the previous technique of negative staining. In that > >> context it is obvious that the vitreous state refers to water, not to the > >> macromolecular species embedded in it: the risk of a potential oxymoron in > >> the crystallographic case arises from trying to choose a single adjective > >> to > >> qualify a two-component sample in which those components behave differently > >> under sudden cooling. > >> > >>I have always found that an expression like "flash-frozen" has a lot > >> going for it: it means that the sample was cooled very quickly, so it > >> describes a process rather than a final state. The fact that this final > >> state preserves the crystalline arrangement of the macromolecule(s), but > >> causes the solvent to go into a vitreous phase, is just part of what every > >> competent reviewer of a crystallographic paper should know, and that ought > >> to avoid the kind of arguments that started this thread. > >> > >> > >>With best wishes, > >> > >> Gerard. > >> > >> -- > >> On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: > >>> Hi Sebastiano, > >>> > >>> I think the term "vitrified crystal" could be understood as a very nice > >>> oxymoron (http://www.oxymoronlist.com/), but it is essentially > >>> self-contradictory and not technically correct. > >>> > >>> As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a > >>> disordered solid state by definition, then it can't be a crystal. A > >>> vitrified crystal would be a crystal which has lost all three-dimensional > >>> ordering, pretty much like the material one gets when using the wrong > >>> "cryo-protectant". > >>> > >>> What one usually does is to soak the crystal in a "cryo-protectant" and > >>> then flash-freeze the resulting material, hoping that the crystal > >>> structure > >>> will be preserved, while the rest remains disordered in a solid state > >>> (vitrified), so that it won't produce a diffraction pattern by itself, and > >>> will hold the crystal in a fixed position (very convenient for data > >>> collection). > >>> > >>> Moreover, I would say that clarifying a material is vitrified when > >>> subjected to liquid N2 temperatures would be required only if you were > >>> working with some liquid solvent which might remain in the liquid phase at > >>> that temperature, instead of the usual solid disordered state, but this is > >>> never the case with protein crystals. > >>> > >>> So, I vote for "frozen crystal".- > >>> > >>> Javier > >>> > >>> > >>> PS: that comment by James Stroud "I forgot to mention that if any > >>> dictionary is an authority on the very cold, it would be the Penguin > >>> dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! > >>> > >>> -- > >>> Javier M. Gonzalez > >>> Protein Crystallography Station >
Re: [ccp4bb] vitrification vs freezing
I was going to mention that too, but since I was a postdoc of Petsko my words could have been viewed as biased. Quyen On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp wrote: > I'm a little confused. Petsko and others were doing > low-temperature/freezing/vitrification crystal experiments in the 1970s, > right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between > what they were doing and what's done now. > > Ron > > On Fri, 16 Nov 2012, Gerard Bricogne wrote: > >> Dear all, >> >>I think we are perhaps being a little bit insular, or blinkered, in >> this discussion. The breakthrough we are talking about, and don't know how >> to call, first occurred not in crystallography but in electron microscopy, >> in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see >> for instance http://www.unil.ch/dee/page53292.html). It made possible the >> direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve >> higher resolution than the previous technique of negative staining. In that >> context it is obvious that the vitreous state refers to water, not to the >> macromolecular species embedded in it: the risk of a potential oxymoron in >> the crystallographic case arises from trying to choose a single adjective to >> qualify a two-component sample in which those components behave differently >> under sudden cooling. >> >>I have always found that an expression like "flash-frozen" has a lot >> going for it: it means that the sample was cooled very quickly, so it >> describes a process rather than a final state. The fact that this final >> state preserves the crystalline arrangement of the macromolecule(s), but >> causes the solvent to go into a vitreous phase, is just part of what every >> competent reviewer of a crystallographic paper should know, and that ought >> to avoid the kind of arguments that started this thread. >> >> >>With best wishes, >> >> Gerard. >> >> -- >> On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: >>> Hi Sebastiano, >>> >>> I think the term "vitrified crystal" could be understood as a very nice >>> oxymoron (http://www.oxymoronlist.com/), but it is essentially >>> self-contradictory and not technically correct. >>> >>> As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a >>> disordered solid state by definition, then it can't be a crystal. A >>> vitrified crystal would be a crystal which has lost all three-dimensional >>> ordering, pretty much like the material one gets when using the wrong >>> "cryo-protectant". >>> >>> What one usually does is to soak the crystal in a "cryo-protectant" and >>> then flash-freeze the resulting material, hoping that the crystal structure >>> will be preserved, while the rest remains disordered in a solid state >>> (vitrified), so that it won't produce a diffraction pattern by itself, and >>> will hold the crystal in a fixed position (very convenient for data >>> collection). >>> >>> Moreover, I would say that clarifying a material is vitrified when >>> subjected to liquid N2 temperatures would be required only if you were >>> working with some liquid solvent which might remain in the liquid phase at >>> that temperature, instead of the usual solid disordered state, but this is >>> never the case with protein crystals. >>> >>> So, I vote for "frozen crystal".- >>> >>> Javier >>> >>> >>> PS: that comment by James Stroud "I forgot to mention that if any >>> dictionary is an authority on the very cold, it would be the Penguin >>> dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! >>> >>> -- >>> Javier M. Gonzalez >>> Protein Crystallography Station >>> Bioscience Division >>> Los Alamos National Laboratory >>> TA-43, Building 1, Room 172-G >>> Mailstop M888 >>> Phone: (505) 667-9376 >>> >>> >>> On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman >>> wrote: >>> "cryopreserved" It says that the crystals were transferred to cryogenic temperatures in an attempt to increase their lifetime in the beam, and avoids all of the other problems with all of the other language described. I was really trying to stay out of this, because I understand what everyone means with all of their other word choices. On Nov 15, 2012, at 2:07 PM, James Stroud wrote: > Isn't "cryo-cooled" redundant? > > James > > On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: > >> Perhaps it's an artisan organic locavore fruit cake. >> >> Either way, your *crystal* is not vitrified. The solvent in your crystal might be glassy but your protein better still hold crystalline order (cf. ice) or you've wasted your time. >> >> Ergo, "cryo-cooled" is the description to use. >> >> Phil Jeffrey >> Princeton >> >> On 11/15/12 1:14 PM, Nukri Sanishvili wrote: >>> s: An alternative way to avoid the argument and discussion a
Re: [ccp4bb] vitrification vs freezing
I'm a little confused. Petsko and others were doing low-temperature/freezing/vitrification crystal experiments in the 1970s, right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between what they were doing and what's done now. Ron On Fri, 16 Nov 2012, Gerard Bricogne wrote: Dear all, I think we are perhaps being a little bit insular, or blinkered, in this discussion. The breakthrough we are talking about, and don't know how to call, first occurred not in crystallography but in electron microscopy, in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see for instance http://www.unil.ch/dee/page53292.html). It made possible the direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve higher resolution than the previous technique of negative staining. In that context it is obvious that the vitreous state refers to water, not to the macromolecular species embedded in it: the risk of a potential oxymoron in the crystallographic case arises from trying to choose a single adjective to qualify a two-component sample in which those components behave differently under sudden cooling. I have always found that an expression like "flash-frozen" has a lot going for it: it means that the sample was cooled very quickly, so it describes a process rather than a final state. The fact that this final state preserves the crystalline arrangement of the macromolecule(s), but causes the solvent to go into a vitreous phase, is just part of what every competent reviewer of a crystallographic paper should know, and that ought to avoid the kind of arguments that started this thread. With best wishes, Gerard. -- On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: Hi Sebastiano, I think the term "vitrified crystal" could be understood as a very nice oxymoron (http://www.oxymoronlist.com/), but it is essentially self-contradictory and not technically correct. As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a disordered solid state by definition, then it can't be a crystal. A vitrified crystal would be a crystal which has lost all three-dimensional ordering, pretty much like the material one gets when using the wrong "cryo-protectant". What one usually does is to soak the crystal in a "cryo-protectant" and then flash-freeze the resulting material, hoping that the crystal structure will be preserved, while the rest remains disordered in a solid state (vitrified), so that it won't produce a diffraction pattern by itself, and will hold the crystal in a fixed position (very convenient for data collection). Moreover, I would say that clarifying a material is vitrified when subjected to liquid N2 temperatures would be required only if you were working with some liquid solvent which might remain in the liquid phase at that temperature, instead of the usual solid disordered state, but this is never the case with protein crystals. So, I vote for "frozen crystal".- Javier PS: that comment by James Stroud "I forgot to mention that if any dictionary is an authority on the very cold, it would be the Penguin dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-43, Building 1, Room 172-G Mailstop M888 Phone: (505) 667-9376 On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman wrote: "cryopreserved" It says that the crystals were transferred to cryogenic temperatures in an attempt to increase their lifetime in the beam, and avoids all of the other problems with all of the other language described. I was really trying to stay out of this, because I understand what everyone means with all of their other word choices. On Nov 15, 2012, at 2:07 PM, James Stroud wrote: Isn't "cryo-cooled" redundant? James On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: Perhaps it's an artisan organic locavore fruit cake. Either way, your *crystal* is not vitrified. The solvent in your crystal might be glassy but your protein better still hold crystalline order (cf. ice) or you've wasted your time. Ergo, "cryo-cooled" is the description to use. Phil Jeffrey Princeton On 11/15/12 1:14 PM, Nukri Sanishvili wrote: s: An alternative way to avoid the argument and discussion all together is to use "cryo-cooled". Tim: You go to a restaurant, spend all that time and money and order a fruitcake? Cheers, N. -- === * * * 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] vitrification vs freezing
I completely agree with Quyen. One of the many definitions of freeze is "to make extremely cold". It is grammatically correct to say "freezing your crystals", especially since, as you point out, everyone reading it knows exactly what you did, and which definition of freeze you were referring too. It is completely unambiguous in my opinion, and it's how people normally talk about it. I wouldn't go into the lab and say "did you cryo-cool those crystals yet?" or "check out this nice crystal. Its ready for vitrification". Best, Kendall On Nov 16, 2012, at 11:28 AM, Quyen Hoang wrote: > I enjoyed following this thread. Because English is not my first language, I > was hoping to learn the official definitions of these terms. > In my opinion, all the variations proposed so far are fine - I don't see > problems with using them. > > For me, when I see "flash frozen in liquid nitrogen" or "flash frozen in > nitrogen stream" I get unambiguous mental images of how the crystals were > prepared. When I hear a policeman yelling "freeze" while pointing a gun (no > personal experience here), there is no ambiguity that I should stop moving > (and won't get confused with cooling myself such that the water in my body > would form hexagonal ice). When I hear that a person is frozen by Parkinson's > disease, there is no ambiguity that his/her muscle had become rigid. > > I think that I will continue to use "flash frozen in liquid nitrogen" or > "flash frozen in nitrogen stream" and I hope that I would not need to explain > to reviewers what that means. > > Quyen > > > > On Nov 16, 2012, at 10:48 AM, Ganesh Natrajan wrote: > >> Hi, >> >> Maybe we could just state the obvious, ie, that the crystals were >> 'Cryo-preserved' in liquid N2. >> >> >> Cheers >> >> Ganesh >> >> Le 16/11/12 16:27, Enrico Stura a écrit : >>> As a referee I also dislike the word "freezing" but only if improperly used: >>> "The crystals were frozen in LN2" is not acceptable because it is the >>> outside >>> liquor that is rapidly cooled to cryogenic temperatures. >>> >>> But the use of "freezing" used as the opposite of "melting" is fine and >>> does not >>> imply a crystalline state. Ice is not always crystalline either: >>> http://en.wikipedia.org/wiki/Amorphous_ice >>> >>>
Re: [ccp4bb] vitrification vs freezing
I enjoyed following this thread. Because English is not my first language, I was hoping to learn the official definitions of these terms. In my opinion, all the variations proposed so far are fine - I don't see problems with using them. For me, when I see "flash frozen in liquid nitrogen" or "flash frozen in nitrogen stream" I get unambiguous mental images of how the crystals were prepared. When I hear a policeman yelling "freeze" while pointing a gun (no personal experience here), there is no ambiguity that I should stop moving (and won't get confused with cooling myself such that the water in my body would form hexagonal ice). When I hear that a person is frozen by Parkinson's disease, there is no ambiguity that his/her muscle had become rigid. I think that I will continue to use "flash frozen in liquid nitrogen" or "flash frozen in nitrogen stream" and I hope that I would not need to explain to reviewers what that means. Quyen On Nov 16, 2012, at 10:48 AM, Ganesh Natrajan wrote: > Hi, > > Maybe we could just state the obvious, ie, that the crystals were > 'Cryo-preserved' in liquid N2. > > > Cheers > > Ganesh > > Le 16/11/12 16:27, Enrico Stura a écrit : >> As a referee I also dislike the word "freezing" but only if improperly used: >> "The crystals were frozen in LN2" is not acceptable because it is the outside >> liquor that is rapidly cooled to cryogenic temperatures. >> >> But the use of "freezing" used as the opposite of "melting" is fine and does >> not >> imply a crystalline state. Ice is not always crystalline either: >> http://en.wikipedia.org/wiki/Amorphous_ice >> >>
Re: [ccp4bb] vitrification vs freezing
Agreed. When we do not know what is actually happening upon cooling in a multi-component system like the crystal, avoiding well -defined terms referring to the state of matter, and instead restricting ourselves to a term describing the process appears less contentious. Thus, flash-cooling, cryo-cooling, cryo-quenching all seem permissible to me as they do not refer to the actual and unknown state of matter. Best regards, BR - Knowledge: When you know a thing, to know that you know it, and when you do not know a thing, to recognize that you do not know it. Conficius. -- -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard Bricogne Sent: Friday, November 16, 2012 3:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] vitrification vs freezing Dear all, I think we are perhaps being a little bit insular, or blinkered, in this discussion. The breakthrough we are talking about, and don't know how to call, first occurred not in crystallography but in electron microscopy, in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see for instance http://www.unil.ch/dee/page53292.html). It made possible the direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve higher resolution than the previous technique of negative staining. In that context it is obvious that the vitreous state refers to water, not to the macromolecular species embedded in it: the risk of a potential oxymoron in the crystallographic case arises from trying to choose a single adjective to qualify a two-component sample in which those components behave differently under sudden cooling. I have always found that an expression like "flash-frozen" has a lot going for it: it means that the sample was cooled very quickly, so it describes a process rather than a final state. The fact that this final state preserves the crystalline arrangement of the macromolecule(s), but causes the solvent to go into a vitreous phase, is just part of what every competent reviewer of a crystallographic paper should know, and that ought to avoid the kind of arguments that started this thread. With best wishes, Gerard. -- On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: > Hi Sebastiano, > > I think the term "vitrified crystal" could be understood as a very > nice oxymoron (http://www.oxymoronlist.com/), but it is essentially > self-contradictory and not technically correct. > > As Ethan said, "vitrify" means "turn into glass". Now, a glass state > is a disordered solid state by definition, then it can't be a crystal. > A vitrified crystal would be a crystal which has lost all > three-dimensional ordering, pretty much like the material one gets > when using the wrong "cryo-protectant". > > What one usually does is to soak the crystal in a "cryo-protectant" > and then flash-freeze the resulting material, hoping that the crystal > structure will be preserved, while the rest remains disordered in a > solid state (vitrified), so that it won't produce a diffraction > pattern by itself, and will hold the crystal in a fixed position (very > convenient for data collection). > > Moreover, I would say that clarifying a material is vitrified when > subjected to liquid N2 temperatures would be required only if you were > working with some liquid solvent which might remain in the liquid > phase at that temperature, instead of the usual solid disordered > state, but this is never the case with protein crystals. > > So, I vote for "frozen crystal".- > > Javier > > > PS: that comment by James Stroud "I forgot to mention that if any > dictionary is an authority on the very cold, it would be the Penguin > dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! > > -- > Javier M. Gonzalez > Protein Crystallography Station > Bioscience Division > Los Alamos National Laboratory > TA-43, Building 1, Room 172-G > Mailstop M888 > Phone: (505) 667-9376 > > > On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman wrote: > > > "cryopreserved" > > > > It says that the crystals were transferred to cryogenic temperatures > > in an attempt to increase their lifetime in the beam, and avoids all > > of the other problems with all of the other language described. > > > > I was really trying to stay out of this, because I understand what > > everyone means with all of their other word choices. > > > > On Nov 15, 2012, at 2:07 PM, James Stroud wrote: > > > > > Isn't "cryo-cooled" redundant? > > > > > > James > > > > > > On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: > > > > > >> Perhaps it's an artisan organic locavore fruit cake. > > >> > > >> Either way, your *crystal* is not vitrified. The solvent in your > > crystal might be glassy but your protein better still hold > > crystalline order (
Re: [ccp4bb] vitrification vs freezing
On Nov 16, 2012, at 10:27 AM, Enrico Stura wrote: > As a referee I also dislike the word "freezing" but only if improperly used: > "The crystals were frozen in LN2" is not acceptable because it is the outside > liquor that is rapidly cooled to cryogenic temperatures. right, while the crystals within the liquor remain at room temperature :) > > But the use of "freezing" used as the opposite of "melting" is fine and does > not > imply a crystalline state. Ice is not always crystalline either: > http://en.wikipedia.org/wiki/Amorphous_ice > > > -- > Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office > Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab > LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE > http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura > http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html > e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] vitrification vs freezing
Hi, Maybe we could just state the obvious, ie, that the crystals were 'Cryo-preserved' in liquid N2. Cheers Ganesh Le 16/11/12 16:27, Enrico Stura a écrit : As a referee I also dislike the word "freezing" but only if improperly used: "The crystals were frozen in LN2" is not acceptable because it is the outside liquor that is rapidly cooled to cryogenic temperatures. But the use of "freezing" used as the opposite of "melting" is fine and does not imply a crystalline state. Ice is not always crystalline either: http://en.wikipedia.org/wiki/Amorphous_ice
Re: [ccp4bb] vitrification vs freezing
As a referee I also dislike the word "freezing" but only if improperly used: "The crystals were frozen in LN2" is not acceptable because it is the outside liquor that is rapidly cooled to cryogenic temperatures. But the use of "freezing" used as the opposite of "melting" is fine and does not imply a crystalline state. Ice is not always crystalline either: http://en.wikipedia.org/wiki/Amorphous_ice -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] vitrification vs freezing
How about Latin? It already has a long and distinguished history of use in science. :) Eric On Fri, Nov 16, 2012 at 4:54 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi James, > > I once heard that in (European) law French is the language of choice > because it were the most precise one (which I find easy to believe). > Maybe we should try and convince journals to only accept articles > written in French - not sure, this will improve their quality, though, > comparing my level of French with my level of English ;-) > > Lovely discussion, > Tim > > On 11/15/2012 09:15 PM, James Stroud wrote: > > On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: > >> I have heard this discussion before and reminds me of people > >> claiming strawberries were nuts - which botanically may be > >> correct, but would still not make me complain about strawberries > >> in a fruit cake I ordered at a restaurant. > >> > >> My Pengiun English Dictionary states (amongst other > >> explanations) freeze: "to make extremely cold", > > > > > > Tim's comment strikes at the heart of the problem. > > > > I think the scientific community should decide a few points. > > > > 1. What is the approved language and dialect for science? 2. Within > > this dialect, what should be the authoritative dictionary? 3. Will > > we allow use of definitions that are not the primary definition > > (second, third, fourth). 4. Will we allow the use of homonyms? 5. > > If not, which homonyms should prevail? > > > > These are all very important questions if we completely disregard > > context in writing. > > > > James > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQpg1XUxlJ7aRr7hoRAl33AKCbSYXQmD2YyVug5s3i+2CYDVDzqQCfZ7Qz > 4IiEP5B5NrB+D0s+r/tIa6o= > =nN9O > -END PGP SIGNATURE- >
Re: [ccp4bb] vitrification vs freezing
HI Tim, you should know better. German is the most precise language, hence all those old German *gosh* books (for the younger readers of this board, there was a time before pdf and Nook readers) for organic chemistry etc. from the 19th century and older (Beilstein, Angewandte ...). And why was that the case ? Because we love-to-connect-three-or-five-words in one describing all of the above :-) how about "data was collected at -180˚C (93.15K)", fairly precise the reader can think if it's frozen or vitrified and the writer couldn't care less. flash-annealing - any takers on that one ? Transition from hexagonal ice to vitrified glass - or just magic ? Jürgen On Nov 16, 2012, at 4:54 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I once heard that in (European) law French is the language of choice because it were the most precise one (which I find easy to believe). Maybe we should try and convince journals to only accept articles written in French - not sure, this will improve their quality, though, comparing my level of French with my level of English ;-) Lovely discussion, Tim On 11/15/2012 09:15 PM, James Stroud wrote: On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: I have heard this discussion before and reminds me of people claiming strawberries were nuts - which botanically may be correct, but would still not make me complain about strawberries in a fruit cake I ordered at a restaurant. My Pengiun English Dictionary states (amongst other explanations) freeze: "to make extremely cold", Tim's comment strikes at the heart of the problem. I think the scientific community should decide a few points. 1. What is the approved language and dialect for science? 2. Within this dialect, what should be the authoritative dictionary? 3. Will we allow use of definitions that are not the primary definition (second, third, fourth). 4. Will we allow the use of homonyms? 5. If not, which homonyms should prevail? These are all very important questions if we completely disregard context in writing. James - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQpg1XUxlJ7aRr7hoRAl33AKCbSYXQmD2YyVug5s3i+2CYDVDzqQCfZ7Qz 4IiEP5B5NrB+D0s+r/tIa6o= =nN9O -END PGP SIGNATURE- .. 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] vitrification vs freezing
Dear all, I surely was not hoping in such a huge response to my original question. I think we all have read excellent contributions, and pleasant posts. Although, as often happens, a unique consensus has not emerged, I have for sure a clearer idea of what I should use in the future, and have learnt a few interesting things. Thank you all for that. It's maybe time to step forward from this thread. Thank you all, once again, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] vitrification vs freezing
Hi Javier, You're on the exact odd nature of crystals of macromolecules, i.e. the solvent content. Small molecule crystallographers have been FREEZING crystals in LiqN2 for data collection long before the method was introduced to macromolecular crystallography. This works perfectly well, since there is no disordered water in those crystals (at least in the ones I'm more familiar with, from my organic chemistry days) and there is no need for any cryoprotectant. In crystals of macromolecules we want to prevent the solvent from freezing and form an ice lattice that will destroy our crystals, hence we use cryoprotectants which cause the ice to be vitirified (maybe, in any case not to crystallize). So we end up with a crystal of macromolecule with vitrified solvent. How we call this entity is one thing and how we call the operation is another thing (some very creative suggestions have been made during the thread). So while vitrified crystal may well sound oxymoron linguistically, it may represent our true reality as protein crystallographers. And finally, I can't resist either: how about vitristal for what we get as the result of cryo-protection and freezing? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Javier Gonzalez [bio...@gmail.com] Sent: Friday, November 16, 2012 8:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] vitrification vs freezing Hi Sebastiano, I think the term "vitrified crystal" could be understood as a very nice oxymoron (http://www.oxymoronlist.com/), but it is essentially self-contradictory and not technically correct. As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a disordered solid state by definition, then it can't be a crystal. A vitrified crystal would be a crystal which has lost all three-dimensional ordering, pretty much like the material one gets when using the wrong "cryo-protectant". What one usually does is to soak the crystal in a "cryo-protectant" and then flash-freeze the resulting material, hoping that the crystal structure will be preserved, while the rest remains disordered in a solid state (vitrified), so that it won't produce a diffraction pattern by itself, and will hold the crystal in a fixed position (very convenient for data collection). Moreover, I would say that clarifying a material is vitrified when subjected to liquid N2 temperatures would be required only if you were working with some liquid solvent which might remain in the liquid phase at that temperature, instead of the usual solid disordered state, but this is never the case with protein crystals. So, I vote for "frozen crystal".- Javier PS: that comment by James Stroud "I forgot to mention that if any dictionary is an authority on the very cold, it would be the Penguin dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-43, Building 1, Room 172-G Mailstop M888 Phone: (505) 667-9376 On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman wrote: "cryopreserved" It says that the crystals were transferred to cryogenic temperatures in an attempt to increase their lifetime in the beam, and avoids all of the other problems with all of the other language described. I was really trying to stay out of this, because I understand what everyone means with all of their other word choices. On Nov 15, 2012, at 2:07 PM, James Stroud wrote: > Isn't "cryo-cooled" redundant? > > James > > On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: > >> Perhaps it's an artisan organic locavore fruit cake. >> >> Either way, your *crystal* is not vitrified. The solvent in your crystal >> might be glassy but your protein better still hold crystalline order (cf. >> ice) or you've wasted your time. >> >> Ergo, "cryo-cooled" is the description to use. >> >> Phil Jeffrey >> Princeton >> >> On 11/15/12 1:14 PM, Nukri Sanishvili wrote: >>> s: An alternative way to avoid the argument and discussion all together >>> is to use "cryo-cooled". >>> Tim: You go to a restaurant, spend all that time and money and order a >>> fruitcake? >>> Cheers, >>> N. >>>
Re: [ccp4bb] vitrification vs freezing
Dear all, I think we are perhaps being a little bit insular, or blinkered, in this discussion. The breakthrough we are talking about, and don't know how to call, first occurred not in crystallography but in electron microscopy, in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see for instance http://www.unil.ch/dee/page53292.html). It made possible the direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve higher resolution than the previous technique of negative staining. In that context it is obvious that the vitreous state refers to water, not to the macromolecular species embedded in it: the risk of a potential oxymoron in the crystallographic case arises from trying to choose a single adjective to qualify a two-component sample in which those components behave differently under sudden cooling. I have always found that an expression like "flash-frozen" has a lot going for it: it means that the sample was cooled very quickly, so it describes a process rather than a final state. The fact that this final state preserves the crystalline arrangement of the macromolecule(s), but causes the solvent to go into a vitreous phase, is just part of what every competent reviewer of a crystallographic paper should know, and that ought to avoid the kind of arguments that started this thread. With best wishes, Gerard. -- On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: > Hi Sebastiano, > > I think the term "vitrified crystal" could be understood as a very nice > oxymoron (http://www.oxymoronlist.com/), but it is essentially > self-contradictory and not technically correct. > > As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a > disordered solid state by definition, then it can't be a crystal. A > vitrified crystal would be a crystal which has lost all three-dimensional > ordering, pretty much like the material one gets when using the wrong > "cryo-protectant". > > What one usually does is to soak the crystal in a "cryo-protectant" and > then flash-freeze the resulting material, hoping that the crystal structure > will be preserved, while the rest remains disordered in a solid state > (vitrified), so that it won't produce a diffraction pattern by itself, and > will hold the crystal in a fixed position (very convenient for data > collection). > > Moreover, I would say that clarifying a material is vitrified when > subjected to liquid N2 temperatures would be required only if you were > working with some liquid solvent which might remain in the liquid phase at > that temperature, instead of the usual solid disordered state, but this is > never the case with protein crystals. > > So, I vote for "frozen crystal".- > > Javier > > > PS: that comment by James Stroud "I forgot to mention that if any > dictionary is an authority on the very cold, it would be the Penguin > dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! > > -- > Javier M. Gonzalez > Protein Crystallography Station > Bioscience Division > Los Alamos National Laboratory > TA-43, Building 1, Room 172-G > Mailstop M888 > Phone: (505) 667-9376 > > > On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman > wrote: > > > "cryopreserved" > > > > It says that the crystals were transferred to cryogenic temperatures in an > > attempt to increase their lifetime in the beam, and avoids all of the other > > problems with all of the other language described. > > > > I was really trying to stay out of this, because I understand what > > everyone means with all of their other word choices. > > > > On Nov 15, 2012, at 2:07 PM, James Stroud wrote: > > > > > Isn't "cryo-cooled" redundant? > > > > > > James > > > > > > On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: > > > > > >> Perhaps it's an artisan organic locavore fruit cake. > > >> > > >> Either way, your *crystal* is not vitrified. The solvent in your > > crystal might be glassy but your protein better still hold crystalline > > order (cf. ice) or you've wasted your time. > > >> > > >> Ergo, "cryo-cooled" is the description to use. > > >> > > >> Phil Jeffrey > > >> Princeton > > >> > > >> On 11/15/12 1:14 PM, Nukri Sanishvili wrote: > > >>> s: An alternative way to avoid the argument and discussion all together > > >>> is to use "cryo-cooled". > > >>> Tim: You go to a restaurant, spend all that time and money and order a > > >>> fruitcake? > > >>> Cheers, > > >>> N. > > >>> > > -- === * * * 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] vitrification vs freezing
What about introducing the use of Franglais in the crystallographic literature ? Ce serait cool ! Fred. On 16/11/12 11:24, Sebastiano Pasqualato wrote: Oui bon d'accord, mais il faudra tout de même décider si utiliser "vitrifiés" ou bien "congelés"... sorry couldn't resist ;-) s On Nov 16, 2012, at 10:54 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I once heard that in (European) law French is the language of choice because it were the most precise one (which I find easy to believe). Maybe we should try and convince journals to only accept articles written in French - not sure, this will improve their quality, though, comparing my level of French with my level of English ;-) Lovely discussion, Tim -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] vitrification vs freezing
Oui bon d'accord, mais il faudra tout de même décider si utiliser "vitrifiés" ou bien "congelés"... sorry couldn't resist ;-) s On Nov 16, 2012, at 10:54 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi James, > > I once heard that in (European) law French is the language of choice > because it were the most precise one (which I find easy to believe). > Maybe we should try and convince journals to only accept articles > written in French - not sure, this will improve their quality, though, > comparing my level of French with my level of English ;-) > > Lovely discussion, > Tim > > On 11/15/2012 09:15 PM, James Stroud wrote: >> On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: >>> I have heard this discussion before and reminds me of people >>> claiming strawberries were nuts - which botanically may be >>> correct, but would still not make me complain about strawberries >>> in a fruit cake I ordered at a restaurant. >>> >>> My Pengiun English Dictionary states (amongst other >>> explanations) freeze: "to make extremely cold", >> >> >> Tim's comment strikes at the heart of the problem. >> >> I think the scientific community should decide a few points. >> >> 1. What is the approved language and dialect for science? 2. Within >> this dialect, what should be the authoritative dictionary? 3. Will >> we allow use of definitions that are not the primary definition >> (second, third, fourth). 4. Will we allow the use of homonyms? 5. >> If not, which homonyms should prevail? >> >> These are all very important questions if we completely disregard >> context in writing. >> >> James >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQpg1XUxlJ7aRr7hoRAl33AKCbSYXQmD2YyVug5s3i+2CYDVDzqQCfZ7Qz > 4IiEP5B5NrB+D0s+r/tIa6o= > =nN9O > -END PGP SIGNATURE- -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] vitrification vs freezing
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I once heard that in (European) law French is the language of choice because it were the most precise one (which I find easy to believe). Maybe we should try and convince journals to only accept articles written in French - not sure, this will improve their quality, though, comparing my level of French with my level of English ;-) Lovely discussion, Tim On 11/15/2012 09:15 PM, James Stroud wrote: > On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: >> I have heard this discussion before and reminds me of people >> claiming strawberries were nuts - which botanically may be >> correct, but would still not make me complain about strawberries >> in a fruit cake I ordered at a restaurant. >> >> My Pengiun English Dictionary states (amongst other >> explanations) freeze: "to make extremely cold", > > > Tim's comment strikes at the heart of the problem. > > I think the scientific community should decide a few points. > > 1. What is the approved language and dialect for science? 2. Within > this dialect, what should be the authoritative dictionary? 3. Will > we allow use of definitions that are not the primary definition > (second, third, fourth). 4. Will we allow the use of homonyms? 5. > If not, which homonyms should prevail? > > These are all very important questions if we completely disregard > context in writing. > > James > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQpg1XUxlJ7aRr7hoRAl33AKCbSYXQmD2YyVug5s3i+2CYDVDzqQCfZ7Qz 4IiEP5B5NrB+D0s+r/tIa6o= =nN9O -END PGP SIGNATURE-
