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 ou

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. ..

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

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

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

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 a

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. E

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 A

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

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 die

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

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:

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

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 "fl

Re: [ccp4bb] vitrification vs freezing

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 han

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 wi

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 be

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 no

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 we

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

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 lea

Re: [ccp4bb] vitrification vs freezing

: 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

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

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 1

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 t

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 wi

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

Re: [ccp4bb] vitrification vs freezing

On 15/11/2012 20:15, 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 orde

Re: [ccp4bb] vitrification vs freezing

"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 eve

Re: [ccp4bb] vitrification vs freezing

CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Stroud [xtald...@gmail.com] Sent: Thursday, November 15, 2012 11:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] vitrification vs freezing Don't you mean Acta Antivitrifica? James On Nov 15, 2012, at 2:05 PM, Boaz Sha

Re: [ccp4bb] vitrification vs freezing

e...@shelx.uni-ac.gwdg.de] > Sent: Thursday, November 15, 2012 10:35 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] vitrification vs freezing > > As usual, Wikipedia has it right: "The antifreeze capabilities of ethylene > glycol have made it an important componen

Re: [ccp4bb] vitrification vs freezing

    From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George Sheldrick [gshe...@shelx.uni-ac.gwdg.de] Sent: Thursday, November 15, 2012 10:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] vitrification vs freezing As usual, Wikipedia has it right: &quo

Re: [ccp4bb] vitrification vs freezing

As usual, Wikipedia has it right: "The antifreeze capabilities of ethylene glycol have made it an important component of vitrification (anticrystallization) mixtures .." Perha

Re: [ccp4bb] vitrification vs freezing

On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: > > My Pengiun English Dictionary states (amongst other explanations) > freeze: "to make extremely cold", I forgot to mention that if any dictionary is an authority on the very cold, it would be the Penguin dictionary. James

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

If Hakon Hope is reading this I can see his eyes rolling back in his head. I vote for "cryo-cooling", since he was one of the inventors of this method, see the following abstract from his 1988 paper in Acta Cryst. B: "Methods have been developed that allow facile X-ray data collection for biolo

Re: [ccp4bb] vitrification vs freezing

Actually, there is a particular kind of "freezing" than can be a good thing: cubic ice. The specific volume of cubic ice is about 2% higher than that of amorphous solid water (or hyperquenched glassy water). In cases where the "preferred" specific volume of the protein lattice is a little b

Re: [ccp4bb] vitrification vs freezing

Hi Ethan, I am not a linguist of Greek or even of English but I would assume that the term "cryo-cooling" is advocated not by DRD but by the people who want to distinguish between cooling down to *cryogenic* temperatures and say, cooling from 25 C to 4 C. Cheers, N. On 11/15/2012 12:45 PM,

Re: [ccp4bb] vitrification vs freezing

talking semantics, kruos (Κρυος), means just cold, not icy cold. Cold in Greece is not nearly icy. Unlike the Netherlands ... it only gets cold when its really icy ;-) Tassos On 15 Nov 2012, at 19:45, Ethan Merritt wrote: > From Greek kruos, icy cold

Re: [ccp4bb] vitrification vs freezing

On Thursday, November 15, 2012 10:14:54 am Raji Edayathumangalam wrote: > Hi Sebastiano, > > Elspeth Garman howls bloody murder everytime someone says they "froze" > their crystals. I think her issue is with the description of the process of > successfully flashcooling crystals in the presence of

Re: [ccp4bb] vitrification vs freezing

Hi Tim, in the UK, you'd probably be rather surprised how many nuts your fruitcake contains, none of them strawberries (thus the saying "as nutty as a fruitcake). Andreas On 15/11/2012 5:59, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear s, I have heard this discu

Re: [ccp4bb] vitrification vs freezing

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 Jeffre

Re: [ccp4bb] vitrification vs freezing

Dear Andrew, I would suggest that Larousse may need to revisit their entry - freeze-drying (in every context I have come across it) refers to lyophilisation, which (i) specifically requires the formation of ice crystals, and (ii) results in the removal of all of the resulting ice from the sample.

Re: [ccp4bb] vitrification vs freezing

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. On 11/15/2012 11:59 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear s, I have

Re: [ccp4bb] vitrification vs freezing

On Thursday, November 15, 2012 09:13:58 am you 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,

Re: [ccp4bb] vitrification vs freezing

Hi Sebastiano, Elspeth Garman howls bloody murder everytime someone says they "froze" their crystals. I think her issue is with the description of the process of successfully flashcooling crystals in the presence of cryoprotectants as "freezing." Freezing technically is understood to imply the for

Re: [ccp4bb] vitrification vs freezing

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 cer

Re: [ccp4bb] vitrification vs freezing

Hi Tim. Well, I surely get your point, but I have to say, that really was the last in the "minor points" addressed by the (again excellent!) referee. That did not bother me at all, I really appreciate a referee that reads thoroughly my paper. Also, it is true we do write in English, but we do

Re: [ccp4bb] vitrification vs freezing

There are implications of ice formation associated with the verb "to freeze" (the OED, for example, includes the following among several definitions of this verb: " Of a liquid, or liquid particles: To be converted into ice." Because the "to make cold" definition that Tim mentioned is also used

Re: [ccp4bb] vitrification vs freezing

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear s, 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 Eng

[ccp4bb] vitrification vs freezing

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