Re: [ccp4bb] vitrification vs freezing

Hi Sebastiano, I think the term "vitrified crystal" could be understood as a very nice oxymoron (http://www.oxymoronlist.com/), but it is essentially self-contradictory and not technically correct. As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a disordered solid state by

Re: [ccp4bb] vitrification vs freezing

On 15/11/2012 20:15, James Stroud wrote: On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: I have heard this discussion before and reminds me of people claiming strawberries were nuts - which botanically may be correct, but would still not make me complain about strawberries in a fruit cake I orde

Re: [ccp4bb] vitrification vs freezing

"cryopreserved" It says that the crystals were transferred to cryogenic temperatures in an attempt to increase their lifetime in the beam, and avoids all of the other problems with all of the other language described. I was really trying to stay out of this, because I understand what eve

Re: [ccp4bb] vitrification vs freezing

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   

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

Re: [ccp4bb] vitrification vs freezing

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  

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: > I have heard this discussion before and reminds me of people claiming > strawberries were nuts - which botanically may be correct, but would > still not make me complain about strawberries in a fruit cake I > ordered at a restaurant. > > My Pengiun

Re: [ccp4bb] vitrification vs freezing

Isn't "cryo-cooled" redundant? James On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: > Perhaps it's an artisan organic locavore fruit cake. > > Either way, your *crystal* is not vitrified. The solvent in your crystal > might be glassy but your protein better still hold crystalline order (cf

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] relations between groups and subgroups?

Everyone knows that there are 230 space groups, and these belong to one of 32 point groups, which, in turn, belong to one of the 14 Bravais lattices, and 7 crystal "systems": triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, rhombohedral and cubic. Or are there? If you look in ${CLI

Re: [ccp4bb] vitrification vs freezing

Perhaps it's an artisan organic locavore fruit cake. Either way, your *crystal* is not vitrified. The solvent in your crystal might be glassy but your protein better still hold crystalline order (cf. ice) or you've wasted your time. Ergo, "cryo-cooled" is the description to use. Phil Jeffre

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

s: An alternative way to avoid the argument and discussion all together is to use "cryo-cooled". Tim: You go to a restaurant, spend all that time and money and order a fruitcake? Cheers, N. On 11/15/2012 11:59 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear s, I have

Re: [ccp4bb] vitrification vs freezing

On Thursday, November 15, 2012 09:13:58 am you wrote: > > Hi folks, > I have recently received a comment on a paper, in which referee #1 (excellent > referee, btw!) commented like this: > > "crystals were vitrified rather than frozen." > > These were crystals grew in ca. 2.5 M sodium malonate,

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

Dear Sebastiano, This is not entirely straight-forward. The Oxford English dictionary gives the first definition of "freeze" relevant to this discussion as: "Of (a body of) water: be converted into or become covered with ice through loss of heat" This is cer

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

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

Re: [ccp4bb] vitrification vs freezing

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear s, I have heard this discussion before and reminds me of people claiming strawberries were nuts - which botanically may be correct, but would still not make me complain about strawberries in a fruit cake I ordered at a restaurant. My Pengiun Eng

[ccp4bb] vitrification vs freezing

Hi folks, I have recently received a comment on a paper, in which referee #1 (excellent referee, btw!) commented like this: "crystals were vitrified rather than frozen." These were crystals grew in ca. 2.5 M sodium malonate, directly dip in liquid nitrogen prior to data collection at 100 K. We

[ccp4bb] Postdoctoral position

A postdoctoral position is available in the Department of Molecular & Cellular Biochemistry, University of Kentucky (http://www.mc.uky.edu/biochemistry/faculty.asp?fid=51). The successful candidate will focus on structure determination of membrane proteins from the ESX (type VII) secretion syst

Re: [ccp4bb] ccp4mg question

On 15/11/2012 13:57, SANCHEZ BARRENA, MARIA JOSE wrote: Dear all, it seems that none of the tricks from Mark or Tim or Stuart´s ccp4mg "making bond" strategy works out... In all cases, the bond is made when drawing in "think/fat band" style... However, when representing in ribbon style, the link

Re: [ccp4bb] ccp4mg question

Dear all, it seems that none of the tricks from Mark or Tim or Stuart´s ccp4mg "making bond" strategy works out... In all cases, the bond is made when drawing in "think/fat band" style... However, when representing in ribbon style, the link is not there... Any other suggestion is welcome! Che

Re: [ccp4bb] ccp4mg question

On 15/11/2012 12:26, SANCHEZ BARRENA, MARIA JOSE wrote: Dear all, I am working with a cyclic protein and I am trying to make a figure with ccp4mg. I would like to know how to say to ccp4mg that the N and C-terminus are bound Although atoms are at a covalent bond distance, the chain is broken

Re: [ccp4bb] ccp4mg question

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Maria, without knowing my guess is that ccp4mg also checks the residue numbers of adjacent residues to decide whether it draws a bond. You might be able to trick ccp4mg by copying the first residue to the C-terminus with identical settings but g

Re: [ccp4bb] ccp4mg question

possible ugly workaround: renumber the pdb file so where ccp4mg thinks the N and C-termini are is hidden in the image you are making (if possible) if you want to make different views you may need to make differently renumbered pdb files. (but probably other people have a smarter way) as an a

[ccp4bb] ccp4mg question

Dear all, I am working with a cyclic protein and I am trying to make a figure with ccp4mg. I would like to know how to say to ccp4mg that the N and C-terminus are bound Although atoms are at a covalent bond distance, the chain is broken by ccp4mg... Many thanks in advance for your suggesti

[ccp4bb] Reminder: BCA Biological Structures Group winter meeting: From Genome to Proteome, 11 Dec 2012

Dear all, This is a friendly reminder that the registration deadline for the BCA Biological Structures Group winter meeting is on 6th Dec 2012, which is now only 3 weeks away. Kind regards, Meindert Original Message Subject: BCA Biological Structures Group winter meeting: F