Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Engin Özkan]

Hi,

I believe this is taken care of automatically if you use phenix to pick 
your free reflections.



From http://www.phenix-online.org/documentation/tutorials/twinning.html


"When a test set is designed, care must be taken that free and work 
reflections are not related by a twin law. The R-free set assignment in 
phenix.refine and phenix.reflection_file_converter is designed with this 
in mind: the free reflections are chosen to obey the highest possible 
symmetry of the lattice."


I believe this applies to all datasets, just in case there may be twinning.

Engin

On 8/27/21 11:12 AM, Jeffrey B Bonanno wrote:

Hi Dirk and Kay,

Excellent, many thanks for the refresher!

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org


-Original Message-
From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
Sent: Friday, August 27, 2021 12:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

CAUTION: This email comes from an external source; the attachments and/or links may 
compromise our secure environment. Do not open or click on suspicious emails. Please 
click on the "Phish Alert" button on the top right of the Outlook dashboard to 
report any suspicious emails.

Dear Jeffrey,

just using thin shells of reflections for the test set might not be enough to 
eliminate any correlation to working set reflections. The distance of the test 
set reflections in reciprocal space, after applying the NCS rotations in 
reciprocal space, to any reflections of the working set should be large enough 
to be uncorrelated. A typical maximum distance for correlation in reciprocal 
space is the first zero (root) of the Fourier transform of the approximated 
spherical shape of the protein molecule, the so-called G-function (see [1) and 
[2]). However, this means, that shells should be thicker than 2 times this 
distance to blindly exclude any potential correlation between test set and 
working set reflection in reciprocal space. This would be way too expensive!

An better way to select uncorrelated reflections is described in [3] (same 
reference that Kay has given), where for each test set reflection, after 
applying the NCS rotations in reciprocal space, the distances to the working 
set reflections are taken into account, and test and working set reflections 
are chosen such that their distances are large enough to be uncorrelated.

Best regards,

Dirk.

[1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962)

[2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966)

[3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006)

On 8/27/21 4:47 PM, Kay Diederichs wrote:

Hi Jeffrey,

good question. Both twinning and NCS may couple reflections across free and 
working sets, and this should be avoided by proper selection - otherwise Rfree 
is biased towards Rwork. Selecting thin shells should be a good option, and can 
be done in SFTOOLS (or DATAMAN, or SHELXPRO).

How much does it matter? Actually I started to search the literature after 
reading your question, and expected that one of Z. Dauter's papers would 
enlighten me, but until a minute ago couldn't find the one(s) that I thought 
existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227-238 which is 
relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta 
Cryst. (2020). D76, 653-667 where they indeed selected thin shells.

Best wishes,
Kay

On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
 wrote:


Hi Kay,

Can you also comment on Rfree set selection? It seems thin shell might be 
preferred in these cases?

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org

##
##

To unsubscribe from the CCP4BB list, click the following link:
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1d
ata=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C34839cf0455841166ca2
08d96974a30a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656772499
344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJ
BTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=XIDw7gK4YhuU02YwVY4F3DyeH
LvPfvamkOvqOnREXWM%3Dreserved=0

This message was issued to members of
https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j
iscmail.ac.uk%2FCCP4BBdata=04%7C01%7Cjeffrey.bonanno%40EINSTEINME
D.ORG%7C34839cf0455841166ca208d96974a30a%7C9c01f0fd65e040c089a82dfd51e
62025%7C0%7C0%7C637656772499344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sda

[ccp4bb] Postdoctoral Research Associate position in Liverpool (corrected)

[Antonyuk, Svetlana]

Postdoctoral Research Associate
University of Liverpool - Department of Cardiovascular and Metabolic Medicine
Location:   Liverpool
Salary: £34,810 to £40,322 p.a.
Hours:  Full Time
Contract Type:  Fixed-Term/Contract
Placed On:  25th August 2021
Closes: 21st September 2021
Job Ref:033448



We are looking for an enthusiastic Post-doctoral Research Associate to join the 
team of Dr Nordine Helassa on a 3-year British Heart Foundation funded project. 
Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease that can 
cause life-threatening cardiac arrythmias. It is the most common cause of 
sudden death in the young and is characterised by ventricular hypertrophy and 
contractile dysfunction. HCM has been associated with mutations in genes mostly 
encoding sarcomeric proteins such as myosin, tropomyosin and troponins. 
However, the detailed molecular mechanism leading to the clinical phenotype 
remains unclear. The project aims to determine the role of disease-associated 
troponin I mutations in cardiac dysfunction using a multidisciplinary approach 
combining protein biophysics, structural biology and muscle physiology.

You will have (or have already submitted) a PhD in structural biology, 
biochemistry, biophysics, biological sciences or a closely allied discipline. 
Laboratory experience with recombinant protein expression/purification 
techniques and structural biology (X-ray and/or NMR) would be advantageous. The 
post is available until 30 November 2024.

For full details and to apply online, please visit: 
https://recruit.liverpool.ac.uk



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




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/