Re: [ccp4bb] vitrification vs freezing

[Jrh]

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

[David Schuller]

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

[Adrian Goldman]

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

[Bryan Lepore]

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

[Quyen Hoang]

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

[Ronald E Stenkamp]

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

[James Stroud]

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

[R. M. Garavito]

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

[Ed Pozharski]

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

[Craig Bingman]

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

[Gerard Bricogne]

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

[Quyen Hoang]

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

[Ronald E Stenkamp]

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

[Kendall Nettles]

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

[Quyen Hoang]

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

[Bernhard Rupp (Hofkristallrat a.D.)]

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:
> >
> >

Re: [ccp4bb] vitrification vs freezing

[Douglas Theobald]

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

[Ganesh Natrajan]

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

[Enrico Stura]

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

[Eric Williams]

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

[Bosch, Juergen]

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

[Sebastiano Pasqualato]

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

[Boaz Shaanan]

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

[Gerard Bricogne]

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

[vellieux]

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

[Sebastiano Pasqualato]

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

[Tim Gruene]

-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

[Javier Gonzalez]

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

[Frank von Delft]

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
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
Hear hear!  I never have the faintest idea what somebody means when they 
say "I froze my crystals".  They may as well be speaking Greek.

Re: [ccp4bb] vitrification vs freezing

[Craig Bingman]

 "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

[Boaz Shaanan]

That's certainly also a good possibility. 


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 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 Shaanan wrote:




And then change the name of the journals to Acta Anticrystallographica A-E


        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 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: "The antifreeze capabilities
 of ethylene glycol have made it an important component of vitrification (anticrystallization)
 mixtures .." 

Perhaps we should call it anticrystallization?

George

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





-- 
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] vitrification vs freezing

[James Stroud]

Don't you mean Acta Antivitrifica?

James

On Nov 15, 2012, at 2:05 PM, Boaz Shaanan wrote:

> And then change the name of the journals to Acta Anticrystallographica A-E
> 
> 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 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: "The antifreeze capabilities of ethylene 
> glycol have made it an important component of vitrification 
> (anticrystallization) mixtures .." 
> 
> Perhaps we should call it anticrystallization?
> 
> George
> 
> 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
>> 
> 
> 
> -- 
> 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] vitrification vs freezing

[Boaz Shaanan]

And then change the name of the journals to Acta Anticrystallographica A-E


        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 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: "The 
antifreeze capabilities of ethylene glycol have made it an important component of

vitrification (anticrystallization) mixtures .." 

Perhaps we should call it anticrystallization?

George

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





-- 
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] vitrification vs freezing

[George Sheldrick]

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


Perhaps we should call it anticrystallization?

George

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




--
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] vitrification vs freezing

[James Stroud]

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

[James Stroud]

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

Re: [ccp4bb] vitrification vs freezing

[James Stroud]

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

[Laurie Betts]

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
biological macromolecules at cryogenic (near liquid N2) temperatures. The
crystals are first transferred from their mother liquor to a hydrocarbon
environment, then mounted with a standard glass fiber (no capillary), and
flash cooled in situ with a cold nitrogen stream on the diffraction
apparatus. This approach prevents freezing of the solvent in the crystals,
so that they maintain their crystallographic integrity. Significant
improvement of resolution can result from the cryogenic data collection,
and radiation damage in the cooled crystals is greatly reduced, or
eliminated, for the duration of data collection."

Laurie Betts

On Thu, Nov 15, 2012 at 1:58 PM, Nukri Sanishvili wrote:

>  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, Ethan Merritt wrote:
>
> 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 cryoprotectants as
> "freezing." Freezing technically is understood to imply the formation of
> hexagonal ice
>
>  Not according to common English usage or any of the dictionaries I
> looked in.
> E.g. American Heritage Dictionary:
>   Freeze 1.a. To pass from the liquid to the solid state by loss of heat.
>
> It needn't refer to water at all, although that is the most common context.
> You can find instructions for freezing olive oil to preserve it;
> when I lived in Madison one occassionally had to worry about frozen
> engine oil;  a headline from earlier this year claimed
> "Russian rivers clogged with frozen oil".
>
>
>  while what one really means is the successful solidification
> of water in a random orientation (vitrification) and the prevention of the
> hexagonal ice.
>
> Semantics semantics!
>
> I'd stick with flashcooled or something along those lines.
> Raji
>
>  Funny you should say that :-)
> While I have never had a referred complain about "frozen" crystals,
> I have had several complain that "flash cooling" is different from
> "immersing in liquid nitrogen".  I never figured out what they had
> in mind, but have since tried to avoid the term flash cooling.
>
> By the way, "cryo-cooled" must be a term advocated by
> The Department of Redundancy Department.
> "cryo" - From Greek kruos, icy cold
>
>   Ethan
>
>
>
> --
> Ruslan Sanishvili (Nukri)
> Macromolecular Crystallographer
> GM/CA@APS
>
> X-ray Science Division, ANL
> 9700 S. Cass Ave.
> Argonne, IL 60439
>
> Tel: (630)252-0665
> Fax: (630)252-0667rsanishv...@anl.gov
>
>

Re: [ccp4bb] vitrification vs freezing

[James Holton]

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 bigger than the "preferred" specific volume of the stuff in the 
solvent channels upon vitrification, a small amount of cubic ice 
"character" can actually make your crystal diffract better.


Basically, a mis-match in the "preferred" volume of the protein and 
solvent creates stress, and stress makes high-angle spots go away (see 
Juers et al. 2001, 2004).  I think this is one of the most 
under-appreciated things about screening for cryos, and seems to be the 
main cause of that mythical "one crystal in a thousand that diffracted 
well" problem.  In my experience, this means you are being very 
consistent in your cryo-cooling but you made one mistake.  Final density 
upon flash-cooling is VERY sensitive to the cooling rate, and little 
things like the thickness of the layer of cold N2 gas above your liquid 
N2 can change the cooling rate by a factor of 100 or so (Warkentin et 
al. 2006).


You can tell if you've got some cubic ice character by looking at the 
background of your diffraction pattern.  Hexagonal ice has three rings 
at 3.45, 3.68, and 3.91 A, whereas cubic ice only has the 3.68 A ring.  
Moreover, noone has ever grown a macroscopic crystal of cubic ice, and 
the smaller the crystallites get, the broader the 3.68 A ring becomes.  
Eventually, it can be hard to tell the difference between 
nano-crystalline cubic ice and the diffuse background expected for 
"amorphous" solvent.  You have to look carefully at the width of the 
"water ring", because the first major diffuse ring from amorphous solid 
water is also at 3.68 A. In fact, all the major diffraction peaks of 
cubic ice are precisely centered on the diffuse rings of amorphous solid 
water. This is perhaps not a coincidence, but it does mean that there is 
a continuum of states between a sharp "ice ring" and an amorphous "water 
ring".  Your best diffraction may well be somewhere in the middle.


-James Holton
MAD Scientist

On 11/15/2012 10:12 AM, 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

[Nukri Sanishvili]

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, Ethan Merritt wrote:

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 cryoprotectants as
"freezing." Freezing technically is understood to imply the formation of
hexagonal ice

Not according to common English usage or any of the dictionaries I
looked in.
E.g. American Heritage Dictionary:
   Freeze 1.a. To pass from the liquid to the solid state by loss of heat.

It needn't refer to water at all, although that is the most common context.
You can find instructions for freezing olive oil to preserve it;
when I lived in Madison one occassionally had to worry about frozen
engine oil;  a headline from earlier this year claimed
"Russian rivers clogged with frozen oil".


while what one really means is the successful solidification
of water in a random orientation (vitrification) and the prevention of the
hexagonal ice.

Semantics semantics!

I'd stick with flashcooled or something along those lines.
Raji

Funny you should say that :-)
While I have never had a referred complain about "frozen" crystals,
I have had several complain that "flash cooling" is different from
"immersing in liquid nitrogen".  I never figured out what they had
in mind, but have since tried to avoid the term flash cooling.

By the way, "cryo-cooled" must be a term advocated by
The Department of Redundancy Department.
"cryo" - From Greek kruos, icy cold

Ethan



--
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov

Re: [ccp4bb] vitrification vs freezing

[Anastassis Perrakis]

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

[Ethan Merritt]

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 cryoprotectants as
> "freezing." Freezing technically is understood to imply the formation of
> hexagonal ice 

Not according to common English usage or any of the dictionaries I
looked in.  
E.g. American Heritage Dictionary:
  Freeze 1.a. To pass from the liquid to the solid state by loss of heat.

It needn't refer to water at all, although that is the most common context.
You can find instructions for freezing olive oil to preserve it;  
when I lived in Madison one occassionally had to worry about frozen 
engine oil;  a headline from earlier this year claimed 
"Russian rivers clogged with frozen oil".

> while what one really means is the successful solidification
> of water in a random orientation (vitrification) and the prevention of the
> hexagonal ice.
> 
> Semantics semantics!
> 
> I'd stick with flashcooled or something along those lines.
> Raji

Funny you should say that :-)
While I have never had a referred complain about "frozen" crystals,
I have had several complain that "flash cooling" is different from
"immersing in liquid nitrogen".  I never figured out what they had
in mind, but have since tried to avoid the term flash cooling.

By the way, "cryo-cooled" must be a term advocated by 
The Department of Redundancy Department.
"cryo" - From Greek kruos, icy cold

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] vitrification vs freezing

[Andreas Förster]

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 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", so as long as you think your article
is written in English, you did not say anything wrong, assuming your
readers are intelligent enough to understand what you are trying to
say - and in a crystallographic article, the process of 'freezing'
your crystal is most likely not your main point where you need to be
100% unambiguous.

Cheers,
Tim



--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] vitrification vs freezing

[Phil Jeffrey]

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

[Tom Murray-Rust]

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.

Tom


>
> 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
>
>
>
>
>
>
>
>
>


-- 
Skype: tom.murray.rust
Twitter: tmurrayrust
http://twitpic.com/photos/tmurrayrust
+44 7970 480 601 (UK)

Re: [ccp4bb] vitrification vs freezing

[Nukri Sanishvili]

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 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", so as long as you think your article
is written in English, you did not say anything wrong, assuming your
readers are intelligent enough to understand what you are trying to
say - and in a crystallographic article, the process of 'freezing'
your crystal is most likely not your main point where you need to be
100% unambiguous.

Cheers,
Tim

On 11/15/2012 06:13 PM, 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


- -- 
Dr Tim Gruene

Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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--
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov

Re: [ccp4bb] vitrification vs freezing

[Ethan Merritt]

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, 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?

What we aim for is vitrification: "to make into a glass".
What we achieve is another matter.
Sometimes dipping into LN2 produces a partially ordered (non-glasslike)
state in the solvent that is bad for our diffraction experiment.

Either result, the desired glass or the unfortunately crystalline ice,
is an example of freezing: "to make into a solid by removing heat".

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] vitrification vs freezing

[Raji Edayathumangalam]

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 formation of
hexagonal ice while what one really means is the successful solidification
of water in a random orientation (vitrification) and the prevention of the
hexagonal ice.

Semantics semantics!

I'd stick with flashcooled or something along those lines.
Raji



On Thu, Nov 15, 2012 at 12:13 PM, Sebastiano Pasqualato <
sebastiano.pasqual...@gmail.com> 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
>
>
>
>
>
>
>
>


-- 
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] vitrification vs freezing

[A Leslie]

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

[Sebastiano Pasqualato]

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 also write of science, and 
that implies being as precise as we can be.

Many have confirmed (thanks Roberto, Mark, Mischa, Henry, Harry, Mathews) that 
"vitrified" is the correct wording, and "cryocooled" could be used as well, 
without being imprecise.

So I just guess I will stick to the new words, happy to have learned something 
new about scientific English.

Thank you too,
ciao,
s

On Nov 15, 2012, at 6:59 PM, Tim Gruene wrote:

> -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 English Dictionary states (amongst other explanations)
> freeze: "to make extremely cold", so as long as you think your article
> is written in English, you did not say anything wrong, assuming your
> readers are intelligent enough to understand what you are trying to
> say - and in a crystallographic article, the process of 'freezing'
> your crystal is most likely not your main point where you need to be
> 100% unambiguous.
> 
> Cheers,
> Tim
> 
> On 11/15/2012 06:13 PM, 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
>> 
>> 
> 
> - -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
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-- 
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

[Patrick Loll]

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, I'd say 
that using freeze to mean vitrify is not absolutely incorrect, but I 
nevertheless avoid it, so as to avoid any suggestion that ice may form (perhaps 
because I'm superstitiously trying to prevent actual ice formation when I cool 
my crystals, or perhaps to avoid problems with fastidious reviewers such as the 
one you've encountered).

May I suggest "flash-cool"?

Pat

On 15 Nov 2012, at 12:13 PM, 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

[Tim Gruene]

-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 English Dictionary states (amongst other explanations)
freeze: "to make extremely cold", so as long as you think your article
is written in English, you did not say anything wrong, assuming your
readers are intelligent enough to understand what you are trying to
say - and in a crystallographic article, the process of 'freezing'
your crystal is most likely not your main point where you need to be
100% unambiguous.

Cheers,
Tim

On 11/15/2012 06:13 PM, 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
> 
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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=R9Wp
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[ccp4bb] vitrification vs freezing

[Sebastiano Pasqualato]

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