Re: [ccp4bb] poll: cutoff for "high resolution"
On 15 May, William Scott wrote: > Actually, if you want to feel really good, I learned (in the context > of optics) that you can resolve two points separated by a distance x > with a diffraction limit of x/0.7, so this means you can start to see > carbon - carbon atomicity at 2.2 Å. This is correct, 2.1 to 2.4 angstroms, and it is the resolution at which the density begins to have a small degree of sphericity, although poor. The sphericity is definitely detectable and sometimes very visible at 2 angstroms which is closer to the determination point of what might be called the atomic pseudo-radius. The atomic position is well determined within this constraint. This is the meaning of over-determined, and possibly a good lower boundary of high resolution atomic structure. A key word here is sphericity, not spherical. Truly spherical density requires better resolution than 2 angstroms, but at the lower limit of over-determination, the density begins to approach the spherical, or a rounded balls and sticks cartoon if you like. High resolution would be that level where the actual atomic positions _begin_ to be apparent as the density begins to approach the spherical. It is over-determined because the atomic coordinate is constrained by the data to be roughly centered within the radius of the theoretical sphere that the density is approaching. Beyond this level of resolution, the density begins to loose sphericity again and enter the realm of ultra-high resolution. The density begins to resolve orbitals. It is a remarkable thing to see. I don't have the exact numbers for distinguishing high versus ultra-high resolution, but this should be specified as well. There is also atomic anisotropy to deal with at better than 2 angstroms resolution, so it is a good thing to get these numbers nailed down with the proper terminology. Regards, Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM Shipping Dock: 1915 E. Madison St. office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ > On May 15, 2008, at 10:12 AM, Gloria Borgstahl wrote: > >> To me, it seems legal to use the words "atomic resolution" once we >> are within the carbon-carbon bond length. So I'm agreeing with Dr. >> Scott. >> Otherwise I'll never get to use the words... >> >> ** >> Gloria Borgstahl >> Eppley Institute for Cancer Research and Allied Diseases >> 987696 Nebraska Medical Center >> 10732A Lied Transplant Center >> Omaha, NE 68198-7696 >> >> http://sbl.unmc.edu >> Office (402) 559-8578 >> FAX (402) 559-3739 >> >> Associate Professor >> Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA >> Metabolism, >> Modulated Crystals, Crystal Perfection, X-ray Topography, >> Interests: ThimbleTack, skateboarding, RAGBRAI, and rollerskating >> ** >> >> >> >> William Scott <[EMAIL PROTECTED]> >> Sent by: CCP4 bulletin board >> 05/15/2008 12:09 PM >> Please respond to >> William Scott <[EMAIL PROTECTED]> >> >> >> To >> CCP4BB@JISCMAIL.AC.UK >> cc >> >> Subject >> Re: [ccp4bb] poll: cutoff for "high resolution" >> >> >> >> >> >> >> On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: >> >>> 1.2A (not surprisingly since this is about the length of covalent >>> bond). >> >> A carbon-carbon single bond is about 1.55 Å. -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- pgpWPfNew1tlt.pgp Description: PGP signature
Re: [ccp4bb] poll: cutoff for "high resolution"
IMHO the word "high" is an useless way to describe your resolution. We're scientists. We measure things. Things called numbers. So why not use them? The words "high" and "low" are about as useful in scientific literature as "large" and "small", "many" and "few", "old" and "new" or the ever-popular "several". I always hate it when I ask my users how big their crystals are and they tell me they are "really small". A "small" crystal in 1988 was 300 um on a side. What is a small crystal now? How about 20 years from now? These things depend on a context that changes over time. There was once a time when 5A was "high resolution" for myoglobin (1955). What is worse about resolution in particular is that the colloquial "high" corresponds to smaller numbers! This DOES confuse people! I'm not saying the words should be banned, but if you are going to use them, you really ought to put it in context. Preferably using Angsroems or at least an SI unit. As for what resolution is "high" (where higher resolution corresponds to smaller d-spacings), you can always look to the PDB for statistics. If you make a histogram of PDB entries vs the "REMARK 2" resolution, then you get a slightly lopsided Gaussian distribution centered at 2.0 A with a width of 1.1 A: http://bl831.als.lbl.gov/~jamesh/pickup/resolution_historgram.png This probably has a lot more to do with the psychology of crystallographers and editors than any kind of physical phenomenon in the crystals. Note the sharp rise crossing over 2.0 A. But if you want to say your resolution is "higher than average", then 2.0 A seems to qualify as the cut-off. If you want to say it is really high, then it is perhaps useful to know that only 10% of the PDB is better than 1.6A and a different 10% is worse than 2.8 A. -James Holton MAD Scientist
Re: [ccp4bb] poll: cutoff for "high resolution"
Hi All, A problem with this is what do we mean by 1.2A data? I/sigma = 2 etc? (not intended to restart the old resolution cutoff discussion) >From a personal point of view, I like to consider what features I can see in the experimental electron density - so relatively high resolution is when I can see the hole (in coot, default I/sig limits) in Phe / Tyr. When I can see both holes in Trp I tend to think of it as really quite high resolution, and when you can tell the difference between C and O in the map from the size of the blobs, well to me that is properly atomic ;o) This probably correlates with the 1.2A rule, anyway. Low resolution data would be, to me, when you can see the main chain but not see the side chains so well. However, this is from somebody who has spent a lot of time looking at structural genomics data, so if you are into membrane proteins etc. your perspective will most likely be different. In passing, it is interesting to take a historical perspective on this and look at some old papers - for example one on phase determination for Myoglobin at a resolution of 2A (Dickerson, Kendrew & Strandberg, 1961, Acta Cryst 14, 1188) where the problem of the number of reflections to consider required a change in approach for the phasing, using a "digital solution" - there were some 9000 or so reflections as opposed to 400 for the 6A structure... Looking at the same problem today, with SAD data to 1.2A, would take several seconds with shelx. Just my 1.5 p worth... Cheers, Graeme 2008/5/15 Bryan W. Lepore <[EMAIL PROTECTED]>: > > On Thu, 15 May 2008, William Scott wrote: > > > On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: > > > > > 1.2A (not surprisingly since this is about the length of covalent > > > bond). > > > > > > > A carbon-carbon single bond is about 1.55 Å. > > > > the van der Waals radius of hydrogen is 1.2A (Eisenberg/Crothers, Pauling, > 1960 ). this distance is referred to in "Sheldrick's 1.2A rule". > > http://scripts.iucr.org/cgi-bin/paper?ad0198 > > -bryan
Re: [ccp4bb] poll: cutoff for "high resolution"
Doesn't this just change the question to "what observation:parameter ratio is needed for my structure to be over-determined?"? As near as I'm aware, the answer to that one seems to be "as many observations as you get". Pete -Original Message- From: CCP4 bulletin board on behalf of [EMAIL PROTECTED] Sent: Thu 5/15/2008 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] poll: cutoff for "high resolution" On 14 May, Mark Del Campo wrote: > At what refinement resolution or resolution ranges would you call a structure > "high resolution" vs. > "low resolution"? I realize that this may boil down to semantics (e.g. some > may classify structures as > "medium resolution"), but I wanted to get an opinion from the pros. A sensible definition of high resolution would be that resolution at which the structure is computationally over-determined, which is about 2 angstroms or better for a complete data set. This would also be a sensible definition for what is called atomic resolution, because the atoms are resolved as spheres or better, so that the position is over-determined. Regards, -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK--
Re: [ccp4bb] poll: cutoff for "high resolution"
On May 15, 2008, at 12:40 PM, Ed Pozharski wrote: I was just trying to protect poor creatures, after all they [hydrogens] only got one electron to hold on to (:-) Ed. A less radical view (pun intended) suggests two. ;)
Re: [ccp4bb] poll: cutoff for "high resolution"
Sure, it has very little to do with original question about what constitutes "high" resolution. And that term is quite relative. 1.8A data is definitely of higher resolution than 2A, but is it "high"? (Not to mention the issue of subjective choice of resolution cutoff). The only way to define these terms is by looking at what is the average resolution in the PDB, and then calling top 25% "high resolution". Perhaps PDB should recalculate this magic number with every release, so that we know what to do (:-) Then, of course, we will have to devise a sliding scale based on resolution, molecule type (aren't protein-DNA complexes on average lower resolution?), etc. We'll call this new field of science resolutionomics. You (and many others) are also quite right that there is a difference between resolution and optical resolution. My quite primitive understanding of it is that you should be able to see local minimum between two peaks to be able to "resolve" them. It appears that hydrogen still retains enough electron density (at least in water) http://academic.reed.edu/chemistry/roco/Density/images/water_rho_relief_large.jpg to form real peaks. If, however, these peaks are watered down by atomic motions, then perhaps hydrogens sometimes could not be "resolved" at all, and thus they are indeed "less equal". I was just trying to protect poor creatures, after all they only got one electron to hold on to (:-) Ed. On Thu, 2008-05-15 at 11:40 -0700, William Scott wrote: > The electrons on the hydrogens won't be centered about the proton > nucleus, so if you want to resolve that as anything more than a bump, > you will need a lot better than 1 Å (or neutrons). But in fairness > the original question asked what you can call "high" resolution, not > what you can call atomic resolution. I think anything better than ~3 > Å should allow unambiguous definition of nucleotide and amino acid > positions. > > > On May 15, 2008, at 11:28 AM, Ed Pozharski wrote: > > > Of course. However, C=0 bond is ~1.2A, and bonds made by those pesky > > hydrogens are ~1A. And I would think (it is semantics again) that to > > reach atomic resolution you have to resolve all atoms, otherwise > > > > "All atoms are equal, but some (non-hydrogens) are more equal than > > others." > > > > Cheers, > > > > Ed. > > > > On Thu, 2008-05-15 at 10:08 -0700, William Scott wrote: > >> On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: > >> > >>> 1.2A (not surprisingly since this is about the length of covalent > >>> bond). > >> > >> A carbon-carbon single bond is about 1.55 Å. > > -- > > Edwin Pozharski, PhD, Assistant Professor > > University of Maryland, Baltimore > > -- > > When the Way is forgotten duty and justice appear; > > Then knowledge and wisdom are born along with hypocrisy. > > When harmonious relationships dissolve then respect and devotion > > arise; > > When a nation falls to chaos then loyalty and patriotism are born. > > -- / Lao Tse / > > > > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] poll: cutoff for "high resolution"
The electrons on the hydrogens won't be centered about the proton nucleus, so if you want to resolve that as anything more than a bump, you will need a lot better than 1 Å (or neutrons). But in fairness the original question asked what you can call "high" resolution, not what you can call atomic resolution. I think anything better than ~3 Å should allow unambiguous definition of nucleotide and amino acid positions. On May 15, 2008, at 11:28 AM, Ed Pozharski wrote: Of course. However, C=0 bond is ~1.2A, and bonds made by those pesky hydrogens are ~1A. And I would think (it is semantics again) that to reach atomic resolution you have to resolve all atoms, otherwise "All atoms are equal, but some (non-hydrogens) are more equal than others." Cheers, Ed. On Thu, 2008-05-15 at 10:08 -0700, William Scott wrote: On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: 1.2A (not surprisingly since this is about the length of covalent bond). A carbon-carbon single bond is about 1.55 Å. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] poll: cutoff for "high resolution"
Of course. However, C=0 bond is ~1.2A, and bonds made by those pesky hydrogens are ~1A. And I would think (it is semantics again) that to reach atomic resolution you have to resolve all atoms, otherwise "All atoms are equal, but some (non-hydrogens) are more equal than others." Cheers, Ed. On Thu, 2008-05-15 at 10:08 -0700, William Scott wrote: > On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: > > > 1.2A (not surprisingly since this is about the length of covalent > > bond). > > A carbon-carbon single bond is about 1.55 Å. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] poll: cutoff for "high resolution"
Optical reconstructions are intensity based. Xtallographic FT are amplitude based. The theoretical value for xray is about 0.9*dmin. Reading: Stenkamp, R.E. and L.H. Jensen. 1984 Resolution revisited. Acta Cryst., A40, 251-254. and the SFCHECK paper for other considerations Vaguine AA, Richelle J, & Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D55, 191-20. BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of William Scott Sent: Thursday, May 15, 2008 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] poll: cutoff for "high resolution" Actually, if you want to feel really good, I learned (in the context of optics) that you can resolve two points separated by a distance x with a diffraction limit of x/0.7, so this means you can start to see carbon - carbon atomicity at 2.2 Å. On May 15, 2008, at 10:12 AM, Gloria Borgstahl wrote: > To me, it seems legal to use the words "atomic resolution" once we are > within the carbon-carbon bond length. So I'm agreeing with Dr. > Scott. > Otherwise I'll never get to use the words... > > ** > > Gloria Borgstahl > Eppley Institute for Cancer Research and Allied Diseases > 987696 Nebraska Medical Center > 10732A Lied Transplant Center > Omaha, NE 68198-7696 > > http://sbl.unmc.edu > Office (402) 559-8578 > FAX (402) 559-3739 > > Associate Professor > Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA > Metabolism, Modulated Crystals, Crystal Perfection, X-ray Topography, > Interests: ThimbleTack, skateboarding, RAGBRAI, and rollerskating > ** > > > > > William Scott <[EMAIL PROTECTED]> Sent by: CCP4 bulletin > board > 05/15/2008 12:09 PM > Please respond to > William Scott <[EMAIL PROTECTED]> > > > To > CCP4BB@JISCMAIL.AC.UK > cc > > Subject > Re: [ccp4bb] poll: cutoff for "high resolution" > > > > > > > On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: > >> 1.2A (not surprisingly since this is about the length of covalent >> bond). > > A carbon-carbon single bond is about 1.55 Å.
Re: [ccp4bb] poll: cutoff for "high resolution"
I don't think the term "high resolution" has any real definition or meaning anymore. If you're proud of the resolution, put the number in the title of the paper and let the reader decide. At one time 2 A was high resolution, but I wouldn't consider that high resolution today for a plain vanilla protein structure. The optical resolution is ~ 0.7 x the spacing at which the diffraction is cut off as a best possible case - SFCHECK gives an estimate of the optical resolution. Since hydrogen atoms are not really visible, even at very high resolution, I'd call atomic resolution that resolution at which atoms in C=O bonds are resolved or ~ 1.2 A. I used to think using atomic resolution as a descriptor was safe (I think the shelx and acorn documentation uses 1.2 A in this definition) until I attended a seminar entitled "Atomic resolution structure of (some membrane protein - I don't remember which one) and found it to be a solid state NMR study where they could figure out the direction in which a helix was running (and could therefore build a helix.) Sue On May 15, 2008, at 9:11 AM, [EMAIL PROTECTED] wrote: On 14 May, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure "high resolution" vs. "low resolution"? I realize that this may boil down to semantics (e.g. some may classify structures as "medium resolution"), but I wanted to get an opinion from the pros. A sensible definition of high resolution would be that resolution at which the structure is computationally over-determined, which is about 2 angstroms or better for a complete data set. This would also be a sensible definition for what is called atomic resolution, because the atoms are resolved as spheres or better, so that the position is over-determined. Regards, -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- Dr. Sue A. Roberts Biochemistry & Biophysics University of Arizona 520 621 8171 [EMAIL PROTECTED]
Re: [ccp4bb] poll: cutoff for "high resolution"
On Thu, 15 May 2008, William Scott wrote: On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: 1.2A (not surprisingly since this is about the length of covalent bond). A carbon-carbon single bond is about 1.55 Å. the van der Waals radius of hydrogen is 1.2A (Eisenberg/Crothers, Pauling, 1960 ). this distance is referred to in "Sheldrick's 1.2A rule". http://scripts.iucr.org/cgi-bin/paper?ad0198 -bryan
Re: [ccp4bb] poll: cutoff for "high resolution"
Actually, if you want to feel really good, I learned (in the context of optics) that you can resolve two points separated by a distance x with a diffraction limit of x/0.7, so this means you can start to see carbon - carbon atomicity at 2.2 Å. On May 15, 2008, at 10:12 AM, Gloria Borgstahl wrote: To me, it seems legal to use the words "atomic resolution" once we are within the carbon-carbon bond length. So I'm agreeing with Dr. Scott. Otherwise I'll never get to use the words... ** Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Associate Professor Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, Crystal Perfection, X-ray Topography, Interests: ThimbleTack, skateboarding, RAGBRAI, and rollerskating ** William Scott <[EMAIL PROTECTED]> Sent by: CCP4 bulletin board 05/15/2008 12:09 PM Please respond to William Scott <[EMAIL PROTECTED]> To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] poll: cutoff for "high resolution" On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: 1.2A (not surprisingly since this is about the length of covalent bond). A carbon-carbon single bond is about 1.55 Å.
Re: [ccp4bb] poll: cutoff for "high resolution"
On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: 1.2A (not surprisingly since this is about the length of covalent bond). A carbon-carbon single bond is about 1.55 Å.
Re: [ccp4bb] poll: cutoff for "high resolution"
I don't think that individual atoms can be RESOLVED at 2A resolution. Even if we forget that hydrogen is also an atom, it is still true that peaks in electron density corresponding to, say, covalently bonded atoms are not separated. If atomic positions at 2A would be over-determined, we won't need geometry restraints. Atomic resolution begins somewhere around 1.2A (not surprisingly since this is about the length of covalent bond). I think there is some confusion regarding the term "atomic resolution" because at some point in the past it signified the ability to refine atomic positions (vs just threading CA backbone through tubes of density). But then I am not old enough to pretend to be an expert on this. Cheers, Ed. On Thu, 2008-05-15 at 12:11 -0400, [EMAIL PROTECTED] wrote: > On 14 May, Mark Del Campo wrote: > > At what refinement resolution or resolution ranges would you call a > > structure "high resolution" vs. > > "low resolution"? I realize that this may boil down to semantics (e.g. > > some may classify structures as > > "medium resolution"), but I wanted to get an opinion from the pros. > > A sensible definition of high resolution would be that resolution at > which the structure is computationally over-determined, which is about > 2 angstroms or better for a complete data set. This would also be a > sensible definition for what is called atomic resolution, because the > atoms are resolved as spheres or better, so that the position is > over-determined. > > Regards, > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] poll: cutoff for "high resolution"
On 14 May, Mark Del Campo wrote: > At what refinement resolution or resolution ranges would you call a structure > "high resolution" vs. > "low resolution"? I realize that this may boil down to semantics (e.g. some > may classify structures as > "medium resolution"), but I wanted to get an opinion from the pros. A sensible definition of high resolution would be that resolution at which the structure is computationally over-determined, which is about 2 angstroms or better for a complete data set. This would also be a sensible definition for what is called atomic resolution, because the atoms are resolved as spheres or better, so that the position is over-determined. Regards, -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- pgpj90Jg8xNX9.pgp Description: PGP signature
Re: [ccp4bb] poll: cutoff for "high resolution"
On May 14, 2008, at 12:28 PM, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure "high resolution" vs. "low resolution"? I realize that this may boil down to semantics (e.g. some may classify structures as "medium resolution"), but I wanted to get an opinion from the pros. This really needs to take into account the numerical resolution vs. inherent-coolness-factor tradeoff matrix. For example, if the macromolecule is comprised of 100% amino acids and catalyzes a reaction in the Krebs cycle, high resolution is 0.5*(C=C), the carbon-carbon double-bond length. If it is a snRNP, 7Å is "moderate resolution."
Re: [ccp4bb] poll: cutoff for "high resolution"
I think this is coupled with the data completeness. Say you have a data 50.0-1.0A resolution, but the completeness in say 3.0-1.0A resolution range is equal to 10%, and it is 100% complete in 50.0-3.0A. Pavel. On 5/14/2008 12:28 PM, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure "high resolution" vs. "low resolution"? I realize that this may boil down to semantics (e.g. some may classify structures as "medium resolution"), but I wanted to get an opinion from the pros.
Re: [ccp4bb] poll: cutoff for "high resolution"
I don't think you can give a resolution range - you could argue that it depends on molecular weight, i.e. high resolution for insulin and high resolution for the ribosome are going to be very different numbers. Other than that, my answer would be that you know it when you've got it :) Cheers, Eddie. Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: [EMAIL PROTECTED] Telepathy: 42.2 GHz Heisenberg was probably here! -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mark Del Campo Sent: Wednesday, May 14, 2008 3:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] poll: cutoff for "high resolution" At what refinement resolution or resolution ranges would you call a structure "high resolution" vs. "low resolution"? I realize that this may boil down to semantics (e.g. some may classify structures as "medium resolution"), but I wanted to get an opinion from the pros.
