Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Fischmann, Thierry]

We should demand that the wwpdb discards all entries that do not satisfy the 
“the criteria of I/SigI > 5 and Rmerge <50%” good practical reference”  . 
That’s probably a majority of them. And of course all associated pubs should be 
retracted, to be consistent with the referee’s attitude of refusing publication 
of new structures that does not fit the “good practical reference”. Ouch!

Either that or the referee’s guidelines should be updated the reflect the most 
up-to-date and accurate practices, like CC1/2, or even (much) better limits as 
determined with STARANISO.

Just IMO.
Thierry

From: CCP4 bulletin board  On Behalf Of Winter, Graeme 
(DLSLtd,RAL,LSCI)
Sent: Friday, February 28, 2020 3:28 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What resolution - X-ray diffraction round this time

EXTERNAL EMAIL – Use caution with any links or file attachments.
Hi Dusan,

I am pretty sure

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

has been considered obsolete for a number of years - the efforts of many have 
shown that this is not good practice, including but not limited to Karplus & 
Diederichs - https://science.sciencemag.org/content/336/6084/1030.long

The suggestion above is to throw away large amounts of almost certainly useful 
information, which cannot give rise to a better model

Best wishes Graeme


On 28 Feb 2020, at 08:22, dusan turk 
mailto:dusan.t...@ijs.si>> wrote:

Hi,

Browsing through the recent discussion on EM data resolution cutoff it occurred 
to me that the X-ray diffraction community isn’t that unanimous either.

My stand:

When the default resolution cutoff provided with the data processing software 
in electron density map calculation and refinement delivers quality maps 
noisier than expected and/or too high R-factors I start adjusting the 
resolution cutoff by lowering the resolution and trying alternative space 
group.   Hence, I allow the data processing programs to suggest where to draw 
the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , 
unless there are problems.

Doing so, I came into a dispute with a referee who shaped his request:

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

So where do we stand? Which are the most objective criteria for resolution 
cutoff to be used in diffraction data processing? Which number of shells to use 
when calculating the statistics? Do we have a consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si<mailto:dusan.t...@ijs.si>
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
   Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com<http://www.skype.com>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




--

This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey

[ccp4bb] AW: [ccp4bb] What resolution - X-ray diffraction round this time

[Schreuder, Herman /DE]

I fully agree with this!
Best, Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Phoebe A. Rice
Gesendet: Freitag, 28. Februar 2020 17:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] What resolution - X-ray diffraction round this 
time

EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk   



Can we get some momentum for the "standard table 1" including TWO numbers - 
outer limit used in refinement, and nominal resolution based on some standard 
such as I/sigI =2 (or 3, or whatever the community can agree on)?  That would 
hopefully cut down on all the reviewer complaints of overstated resolution.



~~~

Phoebe A. Rice

Dept. of Biochem & Mol. Biol. and

  Committee on Microbiology

https://urldefense.proofpoint.com/v2/url?u=https-3A__voices.uchicago.edu_phoebericelab_=DwIGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM=CXNbP2DMixZriXPv1R2bTMMTnMPdy4mwce_8MJuNxlA=

 



On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" 
 wrote:



Dear colleagues,



I agree with all the previous responses, it is a pity to throw away

useful high-resolution data. The problem of high-resolution cutoff

estimation is also nicely summarized in another paper by Andrew Karplus

and Kay Diederichs "Assessing and maximizing data quality in

macromolecular crystallography"


https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4684713_=DwIGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM=lrf35lEnkEOs6pHot-cjxf9f3SI4dmCvkcL4098veOQ=
 . It is suggested

using CC1/2 for the selection of the cutoff for data processing (not

I/sigI or R_whatever). Later on, the decision should be validated

performing the paired refinement protocol.



Good luck with the argumentation.

Martin





On 2/28/20 11:08 AM, LMB wrote:

> Ask the referee - (apart from the other suggestions here)

>

> ‘How would removing data Improve my model?”

>

> Sent from my iPad

>

>> On 28 Feb 2020, at 08:22, dusan turk  wrote:

>>

>> Hi,

>>

>> Browsing through the recent discussion on EM data resolution cutoff

>> it occurred to me that the X-ray diffraction community isn’t that

>> unanimous either.

>>

>> My stand:

>>

>> When the default resolution cutoff provided with the data processing

>> software in electron density map calculation and refinement delivers

>> quality maps noisier than expected and/or too high R-factors I start

>> adjusting the resolution cutoff by lowering the resolution and trying

>> alternative space group. Hence, I allow the data processing programs

>> to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R

>> sym, R p.i.m. and R r.i.m, …) , unless there are problems.

>>

>> Doing so, I came into a dispute with a referee who shaped his request:

>>

>> "It is well accepted that the criteria for resolution cutoff should

>> consider both I/SigI and Rmerge for the outer most shell. For data

>> sets collected at synchrotron sources, the criteria of I/SigI > 5 and

>> Rmerge <50% can be taken as a good practical reference.”

>>

>> So where do we stand? Which are the most objective criteria for

>> resolution cutoff to be used in diffraction data processing? Which

>> number of shells to use when calculating the statistics? Do we have a

>> consensus?

>>

>> best wishes,

>>

>> dusan turk

>>

>>

>>

>> Dr. Dusan Turk, Prof.

>> Head of Structural Biology Group 
https://urldefense.proofpoint.com/v2/url?u=http-3A__stef.ijs.si_=DwIGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM=_3e4jARMhVBSasLY6-m9dOnl_vTRnBGwLgzq_9Dv6c8=

>> Head of Centre for Protein and Structure Production

>> Centre of excellence for Integrated Approaches in Chemistry and

>> Biology of Proteins, Scientific Director

>> 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cipkebip.org_=DwIGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM=78xv1Oze-kc7Gv9avvfnElFBluCHaasC65gzTDktaDM=

>> e-mail: dusan.t...@ijs.si

>> phone: +386 1 477 3857 Dept. of Biochem.&a

Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Diana Tomchick]

But that wouldn’t incorporate other useful information, such as percentage 
completeness in the outer shell and whether inclusion of the reflections in the 
outer shell for refinement actually effects the resulting structural model and 
map to a significant degree.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Feb 28, 2020, at 10:03 AM, Phoebe A. Rice 
mailto:pr...@uchicago.edu>> wrote:

EXTERNAL MAIL

Can we get some momentum for the "standard table 1" including TWO numbers - 
outer limit used in refinement, and nominal resolution based on some standard 
such as I/sigI =2 (or 3, or whatever the community can agree on)?  That would 
hopefully cut down on all the reviewer complaints of overstated resolution.

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
 Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/


On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
martin.m...@ibt.cas.cz> wrote:

   Dear colleagues,

   I agree with all the previous responses, it is a pity to throw away
   useful high-resolution data. The problem of high-resolution cutoff
   estimation is also nicely summarized in another paper by Andrew Karplus
   and Kay Diederichs "Assessing and maximizing data quality in
   macromolecular crystallography"
   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . It is suggested
   using CC1/2 for the selection of the cutoff for data processing (not
   I/sigI or R_whatever). Later on, the decision should be validated
   performing the paired refinement protocol.

   Good luck with the argumentation.
   Martin


   On 2/28/20 11:08 AM, LMB wrote:
Ask the referee - (apart from the other suggestions here)

‘How would removing data Improve my model?”

Sent from my iPad

On 28 Feb 2020, at 08:22, dusan turk 
mailto:dusan.t...@ijs.si>> wrote:

Hi,

Browsing through the recent discussion on EM data resolution cutoff
it occurred to me that the X-ray diffraction community isn’t that
unanimous either.

My stand:

When the default resolution cutoff provided with the data processing
software in electron density map calculation and refinement delivers
quality maps noisier than expected and/or too high R-factors I start
adjusting the resolution cutoff by lowering the resolution and trying
alternative space group. Hence, I allow the data processing programs
to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R
sym, R p.i.m. and R r.i.m, …) , unless there are problems.

Doing so, I came into a dispute with a referee who shaped his request:

"It is well accepted that the criteria for resolution cutoff should
consider both I/SigI and Rmerge for the outer most shell. For data
sets collected at synchrotron sources, the criteria of I/SigI > 5 and
Rmerge <50% can be taken as a good practical reference.”

So where do we stand? Which are the most objective criteria for
resolution cutoff to be used in diffraction data processing? Which
number of shells to use when calculating the statistics? Do we have a
consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and
Biology of Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology
fax: +386 1 477 3984 Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


   -

   Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová 
zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její 
přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu 
nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření 
smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním 
jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní 
odpovědnost Biotechnologického ústavu AV ČR, v. v. i.

   Disclaimer: If not expressly stated otherwise, this e-mail message 
(including any attached files) is intended purely for informational purposes 
and 

Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Phoebe A. Rice]

Can we get some momentum for the "standard table 1" including TWO numbers - 
outer limit used in refinement, and nominal resolution based on some standard 
such as I/sigI =2 (or 3, or whatever the community can agree on)?  That would 
hopefully cut down on all the reviewer complaints of overstated resolution.

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/
 

On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" 
 wrote:

Dear colleagues,

I agree with all the previous responses, it is a pity to throw away
useful high-resolution data. The problem of high-resolution cutoff
estimation is also nicely summarized in another paper by Andrew Karplus
and Kay Diederichs "Assessing and maximizing data quality in
macromolecular crystallography"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . It is suggested
using CC1/2 for the selection of the cutoff for data processing (not
I/sigI or R_whatever). Later on, the decision should be validated
performing the paired refinement protocol.

Good luck with the argumentation.
Martin


On 2/28/20 11:08 AM, LMB wrote:
> Ask the referee - (apart from the other suggestions here)
>
> ‘How would removing data Improve my model?”
>
> Sent from my iPad
>
>> On 28 Feb 2020, at 08:22, dusan turk  wrote:
>>
>> Hi,
>>
>> Browsing through the recent discussion on EM data resolution cutoff
>> it occurred to me that the X-ray diffraction community isn’t that
>> unanimous either.
>>
>> My stand:
>>
>> When the default resolution cutoff provided with the data processing
>> software in electron density map calculation and refinement delivers
>> quality maps noisier than expected and/or too high R-factors I start
>> adjusting the resolution cutoff by lowering the resolution and trying
>> alternative space group. Hence, I allow the data processing programs
>> to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R
>> sym, R p.i.m. and R r.i.m, …) , unless there are problems.
>>
>> Doing so, I came into a dispute with a referee who shaped his request:
>>
>> "It is well accepted that the criteria for resolution cutoff should
>> consider both I/SigI and Rmerge for the outer most shell. For data
>> sets collected at synchrotron sources, the criteria of I/SigI > 5 and
>> Rmerge <50% can be taken as a good practical reference.”
>>
>> So where do we stand? Which are the most objective criteria for
>> resolution cutoff to be used in diffraction data processing? Which
>> number of shells to use when calculating the statistics? Do we have a
>> consensus?
>>
>> best wishes,
>>
>> dusan turk
>>
>>
>>
>> Dr. Dusan Turk, Prof.
>> Head of Structural Biology Group http://stef.ijs.si/
>> Head of Centre for Protein and Structure Production
>> Centre of excellence for Integrated Approaches in Chemistry and
>> Biology of Proteins, Scientific Director
>> http://www.cipkebip.org/
>> e-mail: dusan.t...@ijs.si
>> phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology
>> fax: +386 1 477 3984 Jozef Stefan Institute
>> Jamova 39, 1 000 Ljubljana,Slovenia
>> Skype: dusan.turk (voice over internet: www.skype.com
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


-

Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová 
zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její 
přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu 
nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření 
smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním 
jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní 
odpovědnost Biotechnologického ústavu AV ČR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message 
(including any attached files) is intended purely for informational purposes 
and does not represent a binding agreement on the part of Institute of 
Biotechnology CAS. The text of this message and its attachments cannot be 
considered as a proposal to conclude a contract, nor the acceptance of a 
proposal to conclude a contract, nor any other legal act leading to concluding 
any contract, nor does it create any pre-contractual liability on the part of 

Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Robbie Joosten]

Hi Dusan,

I don't know what the correct answer is but I think it is safe to see that your 
referee has outdated views (trying to stay polite here). I/sigI > 2.0 with 
decent completeness would be not be seen as to agressive by most (but as too 
conservative by others!). From that cut-off you could push the resolution to 
I/sigI > 1.0 by paired refinement and still be safe because you show there is 
useful information in the data.

One thing I do notice that there are still quite a lot of people overstressing 
the resolution in their manuscripts. This causes a lot of unnecessary 
discussion with referees. It is not a well established number, so don't make a 
big deal of it if the point of the paper is about biology rather than methods.

Cheers,
Robbie

On 28 Feb 2020 09:22, dusan turk  wrote:

Hi,

Browsing through the recent discussion on EM data resolution cutoff it occurred 
to me that the X-ray diffraction community isn’t that unanimous either.

My stand:

When the default resolution cutoff provided with the data processing software 
in electron density map calculation and refinement delivers quality maps 
noisier than expected and/or too high R-factors I start adjusting the 
resolution cutoff by lowering the resolution and trying alternative space 
group.   Hence, I allow the data processing programs to suggest where to draw 
the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , 
unless there are problems.

Doing so, I came into a dispute with a referee who shaped his request:

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

So where do we stand? Which are the most objective criteria for resolution 
cutoff to be used in diffraction data processing? Which number of shells to use 
when calculating the statistics? Do we have a consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Dusan,

I am pretty sure

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

has been considered obsolete for a number of years - the efforts of many have 
shown that this is not good practice, including but not limited to Karplus & 
Diederichs - https://science.sciencemag.org/content/336/6084/1030.long

The suggestion above is to throw away large amounts of almost certainly useful 
information, which cannot give rise to a better model

Best wishes Graeme

On 28 Feb 2020, at 08:22, dusan turk 
mailto:dusan.t...@ijs.si>> wrote:

Hi,

Browsing through the recent discussion on EM data resolution cutoff it occurred 
to me that the X-ray diffraction community isn’t that unanimous either.

My stand:

When the default resolution cutoff provided with the data processing software 
in electron density map calculation and refinement delivers quality maps 
noisier than expected and/or too high R-factors I start adjusting the 
resolution cutoff by lowering the resolution and trying alternative space 
group.   Hence, I allow the data processing programs to suggest where to draw 
the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , 
unless there are problems.

Doing so, I came into a dispute with a referee who shaped his request:

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

So where do we stand? Which are the most objective criteria for resolution 
cutoff to be used in diffraction data processing? Which number of shells to use 
when calculating the statistics? Do we have a consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
   Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] What resolution - X-ray diffraction round this time

[dusan turk]

Hi,

Browsing through the recent discussion on EM data resolution cutoff it occurred 
to me that the X-ray diffraction community isn’t that unanimous either.

My stand: 

When the default resolution cutoff provided with the data processing software 
in electron density map calculation and refinement delivers quality maps 
noisier than expected and/or too high R-factors I start adjusting the 
resolution cutoff by lowering the resolution and trying alternative space 
group.   Hence, I allow the data processing programs to suggest where to draw 
the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , 
unless there are problems. 

Doing so, I came into a dispute with a referee who shaped his request: 

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

So where do we stand? Which are the most objective criteria for resolution 
cutoff to be used in diffraction data processing? Which number of shells to use 
when calculating the statistics? Do we have a consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1