Re: [ccp4bb] on the resoution of crystal

[Joel Sussman]

6-Feb-2017
Dear Pavel & Tim,
For a very good visualization & description of “Resolution”,
please see the Proteopedia page created primarily by Eric Martz at:
http://www.proteopedia.org/w/Resolution
it includes a pointer to James Holton’s movie showing an Electron Density Map 
vs. Resolution (with model overlay) going from 0.5Å to 5.Å resolution.
best regards
Joel


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 5Feb, 2017, at 23:44, Tim Gruene 
> wrote:

Dear Pavel,

I believe words have a meaning, but they are not defined. This may make
languages a little more demanding than mathematics, since you have to deal
with a variety of a few hundred thousand to millions, depending how popular
the language in question is, but personally I enjoy the challenge.

W.r.t. the thread, 3.8A resolution is poorer than 1.8A. I understand this is
what John meant to clarify.

Best,
Tim

On Sunday, February 5, 2017 11:12:10 AM CET Pavel Afonine wrote:
Hi Tim, hi Natesh,

one expression is mathematically, the other one is technically 'more

correct'.
I favour the terms poor and good resolution to avoid confusion, or
explicitly
list the values.

just out of curiosity.. what's your definition of 'poor' and 'good'
resolutions? I suspect there are as many definitions as many subscribers to
this list are -;)

One way to quantify resolution is that what kind of detail you can see in
the map, like for example:

- deformation density (~0.7A and higher) = ultra-high, sub-atomic,
sub-Angstrom;
- H atoms (~0.9A and higher) = not sure what the name is;
- individual non-H atoms (~1.2A and higher) = atomic;
- hole in rings (~2A and higher?) = high;
- medium;
- still can see side chains (up to 4.5A);
- no side-chains but SS elements (such as tubes of density for helices) =
low
- no SS, molecular envelopes = very low.

Note, resolution alone is not a good measure though. Data completeness is
similarly important, e.g. a map corresponding to 2A resolution may look
like a 3ish A resolution if you miss some low-resolution data or
high-resolution end is severely incomplete (Acta Cryst. (2014). D70,
2593-2606).

Low resolution  --> worse than 2.7 A

Ultra high resolution --> better than 0.95 A

Looking into this in some systematic way one can define low-resolution as
6A and lower, and ultra-high resolution as 0.7A and higher (Page 1291: Acta
Cryst. (2009). D65, 1283–1291).

All the best,
Pavel

--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Re: [ccp4bb] on the resoution of crystal

[Tim Gruene]

Dear Pavel,

I believe words have a meaning, but they are not defined. This may make 
languages a little more demanding than mathematics, since you have to deal 
with a variety of a few hundred thousand to millions, depending how popular 
the language in question is, but personally I enjoy the challenge.

W.r.t. the thread, 3.8A resolution is poorer than 1.8A. I understand this is 
what John meant to clarify.

Best,
Tim

On Sunday, February 5, 2017 11:12:10 AM CET Pavel Afonine wrote:
> Hi Tim, hi Natesh,
> 
> one expression is mathematically, the other one is technically 'more
> 
> > correct'.
> > I favour the terms poor and good resolution to avoid confusion, or
> > explicitly
> > list the values.
> 
> just out of curiosity.. what's your definition of 'poor' and 'good'
> resolutions? I suspect there are as many definitions as many subscribers to
> this list are -;)
> 
> One way to quantify resolution is that what kind of detail you can see in
> the map, like for example:
> 
> - deformation density (~0.7A and higher) = ultra-high, sub-atomic,
> sub-Angstrom;
> - H atoms (~0.9A and higher) = not sure what the name is;
> - individual non-H atoms (~1.2A and higher) = atomic;
> - hole in rings (~2A and higher?) = high;
> - medium;
> - still can see side chains (up to 4.5A);
> - no side-chains but SS elements (such as tubes of density for helices) =
> low
> - no SS, molecular envelopes = very low.
> 
> Note, resolution alone is not a good measure though. Data completeness is
> similarly important, e.g. a map corresponding to 2A resolution may look
> like a 3ish A resolution if you miss some low-resolution data or
> high-resolution end is severely incomplete (Acta Cryst. (2014). D70,
> 2593-2606).
> 
> Low resolution  --> worse than 2.7 A
> 
> > Ultra high resolution --> better than 0.95 A
> 
> Looking into this in some systematic way one can define low-resolution as
> 6A and lower, and ultra-high resolution as 0.7A and higher (Page 1291: Acta
> Cryst. (2009). D65, 1283–1291).
> 
> All the best,
> Pavel

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


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Re: [ccp4bb] on the resoution of crystal

[Pavel Afonine]

Hi Tim, hi Natesh,

one expression is mathematically, the other one is technically 'more
> correct'.
> I favour the terms poor and good resolution to avoid confusion, or
> explicitly
> list the values.


just out of curiosity.. what's your definition of 'poor' and 'good'
resolutions? I suspect there are as many definitions as many subscribers to
this list are -;)

One way to quantify resolution is that what kind of detail you can see in
the map, like for example:

- deformation density (~0.7A and higher) = ultra-high, sub-atomic,
sub-Angstrom;
- H atoms (~0.9A and higher) = not sure what the name is;
- individual non-H atoms (~1.2A and higher) = atomic;
- hole in rings (~2A and higher?) = high;
- medium;
- still can see side chains (up to 4.5A);
- no side-chains but SS elements (such as tubes of density for helices) =
low
- no SS, molecular envelopes = very low.

Note, resolution alone is not a good measure though. Data completeness is
similarly important, e.g. a map corresponding to 2A resolution may look
like a 3ish A resolution if you miss some low-resolution data or
high-resolution end is severely incomplete (Acta Cryst. (2014). D70,
2593-2606).

Low resolution  --> worse than 2.7 A
> Ultra high resolution --> better than 0.95 A
>

Looking into this in some systematic way one can define low-resolution as
6A and lower, and ultra-high resolution as 0.7A and higher (Page 1291: Acta
Cryst. (2009). D65, 1283–1291).

All the best,
Pavel

Re: [ccp4bb] on the resoution of crystal

[Natesh Ramanathan]

Dear John,

  In protein crystallography, the ranges customarily applied to
resolution are:

 Low resolution  --> worse than 2.7 A
 Medium resolution -->  better than 2.7 A but worse than 1.8 A
 High resolution -->  better than 1.8 Aand worse than 1.2 A
 Atomic resolution --> better than 1.2 A  and worse than 0.95 A
Ultra high resolution --> better than 0.95 A

There is a very nice diagram for you in Fig. 5 of  Wlodawer et al., FEBS J.
2008 Jan; 275(1): 1–21.
:
at this link:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465431/figure/F5/

   You should think in terms of reciprocal space and diffraction.
Higher angle of diffraction w.r.t. the incident beam means High Resolution,
which means lower number.

Best wishes,
Natesh

On 5 February 2017 at 17:39,  <
0ef8f1cfe4cc-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All,
>
> For one protein crystal, its resolution was 1.8 A. For another crystal for
> the same protein,  its resolution was 3.8 A. In literature, do we call the
> 1.8 A crystal as the high resolution crystal (because of quality), or do we
> call the 3.8 A crystal as the high resolution crystal (because of 3.8 was
> larger than 1,8)?
>
> Best regards.
>
> John
>



-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Ramalingaswami Fellow-DBT, Assistant Professor
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
1st floor, Dept. of Computer Science & Engg. Building,
CET Campus, Engineering College P.O.,
Trivandrum,  695016, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
http://faculty.iisertvm.ac.in/~natesh
Ph. 0091- 471-2599403
Fax.0091-471-2597427

Re: [ccp4bb] on the resoution of crystal

[Tim Gruene]

Dear John,

one expression is mathematically, the other one is technically 'more correct'. 
I favour the terms poor and good resolution to avoid confusion, or explicitly 
list the values.

Best,
Tim

On Sunday, February 5, 2017 12:09:11 PM CET  wrote:
>  Dear All,
> For one protein crystal, its resolution was 1.8 A. For another crystal for
> the same protein,  its resolution was 3.8 A. In literature, do we call the
> 1.8 A crystal as the high resolution crystal (because of quality), or do we
> call the 3.8 A crystal as the high resolution crystal (because of 3.8 was
> larger than 1,8)? Best regards.
> John

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


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Re: [ccp4bb] on the resoution of crystal

[Dale Tronrud]

   It is confusing, but "high" is meant to indicate the quality of the
final electron density map based on the data.  Your 1.8 A data set will
give the better map, and is the high resolution data set.

Dale Tronrud

On 2/5/2017 4:09 AM,  wrote:
> Dear All,
> 
> For one protein crystal, its resolution was 1.8 A. For another crystal
> for the same protein,  its resolution was 3.8 A. In literature, do we
> call the 1.8 A crystal as the high resolution crystal (because of
> quality), or do we call the 3.8 A crystal as the high resolution crystal
> (because of 3.8 was larger than 1,8)?
> 
> Best regards.
> 
> John

[ccp4bb] on the resoution of crystal

 Dear All,
For one protein crystal, its resolution was 1.8 A. For another crystal for the 
same protein,  its resolution was 3.8 A. In literature, do we call the 1.8 A 
crystal as the high resolution crystal (because of quality), or do we call the 
3.8 A crystal as the high resolution crystal (because of 3.8 was larger than 
1,8)?
Best regards.
John