[ccp4bb] Three Postdoctoral positions and one predoc position now available at EMBL Hamburg Unit

2013-08-14 Thread margret


We would like to draw your attention to the following three postdoctoral 
and 1 postdoctoral position open at the EMBL Hamburg Unit. Further 
details can be found below.

regards
Margret

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked 
scientific research organisations in the world. The Headquarters Laboratory is 
located in Heidelberg (Germany), with additional sites in Grenoble (France), 
Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy). The main research 
focus of the EMBL Hamburg Unit is in challenging structural biology.  The 
following fellowships are available in the research group of Matthias Wilmanns:
 


*Postdoctoral Fellowship:*  Structural/Functional Studies on Proteins of the 
Peroxisomal Proliferation Machinery
Project outline: Proteins Pex11p and Pex25p are critically involved in the 
proliferation of peroxisomes. We would like to determine the structures of 
these proteins, possibly in complex with further peroxins, and complement 
structural work with in vivo functional characterization, in cooperation with 
partners of the EC ITN Network PERFUME (www.itn-perfume.eu).

*Postdoctoral Fellowship*: Structure of the Complete Pex5p-Pex14p Protein 
Translocon Complex  Cargo Complexes
Project Outline: To date, the overall structure of the peroxisomal translocon, 
a multi protein component complex across the peroxisomal membrane remains 
unknown. We are aiming to determine the structure of the minimal Pex5p-Pex14p 
protein translocon by a hybrid structural biology approach, including: X-ray 
crystallography, small angle X-ray scattering, biophysical methods, 
cross-linking, and electron microscopy (optional). In collaboration with 
partners of the peroxisomal network PerTrans we will raise structure-based 
hypotheses, to be investigated with a range of functional approaches
 
*Postdoctoral Fellowship*: Structure of the Human Peroxisomal PTS2 Receptor in the Presence of Co-receptors  Cargos  
Project Outline: Peroxisomal matrix proteins are recognized by two principle peroxisomal receptor, recognising protein targets either with a PTS1 or with a PTS2 motif. We are aiming to determine the structure of the human peroxisomal PTS2 receptor in the presence of co-receptors and cargos. In collaboration with partners of the peroxisomal network PerTrans we will raise structure-based hypotheses, to be investigated with a range of functional approaches.


*Informal inquiries should be sent to: wilma...@embl-hamburg.de
**For all three postdoc positions, please apply online throughwww.embl.org/jobs*
*Closing date for all fellowships: 15 September 2013
*
For further information:http://www.embl-hamburg.de/aboutus/jobs/
 



*Predoctoral fellowship*  (jointly with Henry Chapman, CFEL and University of 
Hamburg): In situ crystallization in peroxisomes  Project Outline: We would 
like to explore yeast peroxisomes as nucleation host for crystallization, 
leading to novel applications in structural biology. Expertise required: 
molecular biology, protein expression and purification, biochemistry. 
Additional expertise would be advantageous: crystallization, structural biology 
techniques, genetics. The project will provide an unique opportunity to become 
acquainted with established and emerging structural methods such the X-ray free 
electron laser, and X-ray imaging. This PhD thesis research project is part of 
the Center for Ultrafast Imaging at the University of Hamburg and will be 
co-directed by Matthias Wilmanns, EMBL, and Henry Chapman, DESY. For 
applications please go tohttp://www.cui.uni-hamburg.de/en/phd-positions/. 
Informal inquiries should be sent to:wilma...@embl-hamburg.de
 





[ccp4bb] Vacancy: Professor for Biophysics at University of Konstanz

2013-08-14 Thread Kay Diederichs

Hi everybody,

I would like to bring to your attention the following job offer:
==

The University of Konstanz with its “Institutional Strategy to promote 
Top-Level Research” has been receiving continuous funding since 2007 
within the framework of the Excellence Initiative by the German Federal 
and State Governments.


The Faculty of Sciences, Department of Biology, seeks to fill a

W 3-Full Professorship of Biophysics

Applicants should work and be internationally recognized in the field of 
Biophysics, preferentially in structure determination of proteins. The 
applicant should be able to participate in Research Consortia (e.g. 
Collaborative Research Center (SFB969) on “Chemical and Biological 
Principles of Cellular Proteostasis” and the Graduate School GSC 218 
„Konstanz Research School Chemical Biology”). The incumbent professor is 
expected to teach Biophysics at the bachelor’s and master’s level.


Selected candidates will be invited to a scientific colloquium to be 
held in Konstanz in the winter term 2013/2014.


The University of Konstanz is an equal opportunity employer and tries to 
increase the number of women in research and teaching.


The University of Konstanz encourages disabled people to apply. They 
will be given preference if appropriately qualified.


The University of Konstanz has been certified as a family-friendly 
institution by the Hertie Foundation and is committed to further the 
compatibility of work and family life.


The University of Konstanz offers a „Dual Career Program“. Information 
can be obtained from: http://www.uni-konstanz.de/dcc .


Applications comprising a curriculum vitae, publication list, a list of 
grants and awards, details of teaching experience, as well as statements 
of current research topics, future research directions and interests 
(see pdf-link below on our website) should be sent electronically until 
15 September 2013 under the reference number 2013/136 formatted into one 
pdf-file to: prof-2013-...@uni-konstanz.de .


Further information is available on our website: 
http://www.uni-konstanz.de/stellen or by contacting Mr. Hanns Fahlbusch 
by e-mail: hanns.fahlbu...@uni-konstanz.de .

=

An application cover form (PDF) can be downloaded from 
http://www.uni-konstanz.de/stellenangebote/?cont=stellauswseite=2013/136id=3 
.

--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz


[ccp4bb] BBSRC- funded PDRA post on heme enzymes at Leicester

2013-08-14 Thread Peter Moody
The project will involve structural, functional and mechanistic studies on
different heme proteins, including neutron crystallography and single
crystal resonance Raman spectroscopy. This work is a collaboration of
Peter Moody in the Department of Biochemistry and  Emma Raven in the
Department of Chemistry (but we are in the same building).

The link is
http://ig5.i-grasp.com/fe/tpl_UniversityOfLeicester01.asp?s=4A515F4E5A565B1Ajobid=82300,2348228658key=78315784c=786021238234pagestamp=sevlztwcyjtrujnidq


Informal enquiries are welcome, but please use my universiy email (
peter.mo...@le.ac.uk) not this one.

Peter Moody
1/56 Henry Wellcome Laboratories
University of Leicester
Lancaster Road
Leicester
LE1 9HN
UK
tel. (0)116 229 7097


http://www2.le.ac.uk/departments/biochemistry/staff/moodyredir.aspx?C=7h19pcspqEmPAALvHREjMjo_krJWbNBI_LMEQufsD8fcXnwT9NTTIL6o7-nOe5BjK9EY1boVZ6U.URL=http%3a%2f%2fwww2.le.ac.uk%2fdepartments%2fbiochemistry%2fstaff%2fmoody


[ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Yafang Chen
Dear All,

I recently processed a dataset, in which I/sigmaI of the last shell is 2.3,
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0?
The completeness is 100 (100). Thank you so much for your help in advance!

Best,
Yafang

-- 
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Yafang,

a mathematically simple answer would be you collected no symmetry
equivalent reflections, although experimentally this is probably
difficult to achieve, unless your space group is P1. If you could tell
the name of the software you used, the respective developers might
know if '0' indicates something specific.

Regards,
Tim

On 08/14/2013 04:59 PM, Yafang Chen wrote:
 Dear All,
 
 I recently processed a dataset, in which I/sigmaI of the last shell
 is 2.3, while Rmerge of the last shell is 0. Does anyone know why
 the Rmerge is 0? The completeness is 100 (100). Thank you so much
 for your help in advance!
 
 Best, Yafang
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.14 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFSC6C5UxlJ7aRr7hoRAvgiAJ9uGurdV1F1NbwMShnGBQforDPnGgCg7IZ7
6lz3MWS/qAsmAsX6Wf8f4Tg=
=l/px
-END PGP SIGNATURE-


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Phil Evans
multiplicity = 1.0?

On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com wrote:

 Dear All,
 
 I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, 
 while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? 
 The completeness is 100 (100). Thank you so much for your help in advance!
 
 Best,
 Yafang
 
 -- 
 Yafang Chen
  
 Graduate Research Assistant
 Mesecar Lab
 Department of Biological Sciences
 Purdue University
 Hockmeyer Hall of Structural Biology
 240 S. Martin Jischke Drive
 West Lafayette, IN 47907


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Yafang Chen
Dear All,

Here are some more details about the question I asked earlier about Rmerge
is 0 in the last shell. I processed the data using HKL2000. The space
group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is
6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not
to cut back the resolution any more. But I don't know how to explain Rmerge
in the last shell being 0. Besides, I am wondering if this data is
publishable (with Rmerge being 0 in the last shell). Thank you so much for
your help!

Best,
Yafang


On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.comwrote:

 Dear All,

 I recently processed a dataset, in which I/sigmaI of the last shell is
 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge
 is 0? The completeness is 100 (100). Thank you so much for your help in
 advance!

 Best,
 Yafang

 --
 Yafang Chen

 Graduate Research Assistant
 Mesecar Lab
 Department of Biological Sciences
 Purdue University
 Hockmeyer Hall of Structural Biology
 240 S. Martin Jischke Drive
 West Lafayette, IN 47907




-- 
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Jeffrey, Philip D.
Hello Yafang,

The answer lies in the fact that you used HKL2000.  Scalepack has a long 
standing feature where it reports Rmerge  100% as zero.  Quite why they do 
that is a mystery, but your Rmerge in the outermost shell is NOT zero - the 
Rmerge for the lower resolution shells will show up as non-zero if Rmerge  
100%.

That feature is overdue for a fix.

Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import 
into CCP4 via Pointless and have Scala or Aimless report the correct 
statistics.  Reprocessing the data using XDS or Mosflm will ultimately lead you 
to scaling the data with a program that doesn't have that bug.  If you do this, 
report Rmeas rather than Rmerge, the former being a better measure.

Phil Jeffrey
Princeton



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen 
[yafangche...@gmail.com]
Sent: Wednesday, August 14, 2013 11:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rmerge of the last shell is zero

Dear All,

Here are some more details about the question I asked earlier about Rmerge is 
0 in the last shell. I processed the data using HKL2000. The space group is 
I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). 
Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back 
the resolution any more. But I don't know how to explain Rmerge in the last 
shell being 0. Besides, I am wondering if this data is publishable (with Rmerge 
being 0 in the last shell). Thank you so much for your help!

Best,
Yafang


On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen 
yafangche...@gmail.commailto:yafangche...@gmail.com wrote:
Dear All,

I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, 
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The 
completeness is 100 (100). Thank you so much for your help in advance!

Best,
Yafang

--
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907



--
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Pietro Roversi
HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100%

OUCH

Sent from my Desktop

Dr. Pietro Roversi
Oxford University Biochemistry Department - Glycobiology Division
South Parks Road
Oxford OX1 3QU England - UK
Tel. 0044 1865 275339

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen 
[yafangche...@gmail.com]
Sent: 14 August 2013 16:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rmerge of the last shell is zero

Dear All,

Here are some more details about the question I asked earlier about Rmerge is 
0 in the last shell. I processed the data using HKL2000. The space group is 
I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). 
Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back 
the resolution any more. But I don't know how to explain Rmerge in the last 
shell being 0. Besides, I am wondering if this data is publishable (with Rmerge 
being 0 in the last shell). Thank you so much for your help!

Best,
Yafang


On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen 
yafangche...@gmail.commailto:yafangche...@gmail.com wrote:
Dear All,

I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, 
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The 
completeness is 100 (100). Thank you so much for your help in advance!

Best,
Yafang

--
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907



--
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907


[ccp4bb] New wwPDB X-ray structure validation reports

2013-08-14 Thread Gary Battle
The wwPDB partners are pleased to announce that new X-ray structure 
validation reports are now being provided to depositors as part of the 
structure annotation process. For the full announcement, see: 
http://www.wwpdb.org/news/news_2013.html#02-August-2013


The reports can be used by depositors to assess the quality of their 
structures, and by journal editors and referees as a useful tool in the 
manuscript-review process.


“Validation ‘at the gate’ is crucial to improving the quality and 
consistency of the structural archive,” said Gerard Kleywegt, Head of 
PDBe. “The new wwPDB validation reports for X-ray crystal structures 
draw on a wealth of community experience in the validation of models, 
experimental data and the fit of the model to these data. The new style 
reports are a huge improvement compared to the reports previously 
provided by the wwPDB partners. Initial feedback from depositors, 
annotation staff and users alike has been very positive and this has in 
fact motivated us to start delivering the reports much earlier than we 
had planned. We strongly encourage journal editors and referees to 
request these reports from depositors as part of the manuscript 
submission and review process.”


The new X-ray structure validation reports have been prepared according 
to the recommendations of the wwPDB X-ray Validation Task Force and 
provide an assessment of structure quality using widely accepted 
standards and criteria. Crucially, the new reports also provide an 
easily interpretable graphic that compares the quality of a structure to 
that of other structures in the PDB archive and to structures of similar 
resolution.


Further information, including sample X-ray validation reports, is 
available at http://www.wwpdb.org/validation.html


We would welcome your feedback on the new style validation reports. 
Please send any comments, questions or suggestions to 
validat...@mail.wwpdb.org


Gary Battle
on behalf of the wwPDB


Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread James Holton
No matter what the value printed out for Rmerge in the outer shell is, I
recommend using - or n/a in your paper.  This is because
sum(|I-I0|)/sum(I) actually is equal to n/a when sum(I) = 0.

-James Holton
MAD Scientist



On Wed, Aug 14, 2013 at 8:41 AM, Pietro Roversi 
pietro.rove...@bioch.ox.ac.uk wrote:

 HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100%

 OUCH

 Sent from my Desktop

 Dr. Pietro Roversi
 Oxford University Biochemistry Department - Glycobiology Division
 South Parks Road
 Oxford OX1 3QU England - UK
 Tel. 0044 1865 275339
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang
 Chen [yafangche...@gmail.com]
 Sent: 14 August 2013 16:32
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Rmerge of the last shell is zero

 Dear All,

 Here are some more details about the question I asked earlier about
 Rmerge is 0 in the last shell. I processed the data using HKL2000. The
 space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3).
 Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I
 preferred not to cut back the resolution any more. But I don't know how to
 explain Rmerge in the last shell being 0. Besides, I am wondering if this
 data is publishable (with Rmerge being 0 in the last shell). Thank you so
 much for your help!

 Best,
 Yafang


 On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com
 mailto:yafangche...@gmail.com wrote:
 Dear All,

 I recently processed a dataset, in which I/sigmaI of the last shell is
 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge
 is 0? The completeness is 100 (100). Thank you so much for your help in
 advance!

 Best,
 Yafang

 --
 Yafang Chen

 Graduate Research Assistant
 Mesecar Lab
 Department of Biological Sciences
 Purdue University
 Hockmeyer Hall of Structural Biology
 240 S. Martin Jischke Drive
 West Lafayette, IN 47907



 --
 Yafang Chen

 Graduate Research Assistant
 Mesecar Lab
 Department of Biological Sciences
 Purdue University
 Hockmeyer Hall of Structural Biology
 240 S. Martin Jischke Drive
 West Lafayette, IN 47907



Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Frank von Delft
This HKL2000 (scalepack) feature is actually extremely sensible:  an 
Rmerge that high is mathematically meaningless, it quite literally tells 
you nothing at all about he signal in your data.


So I second James's advice:  just put n/a in your table 1.

If the reviewer complains, point them to Karplus  Diederichs, Science, 
2012, and Evans and Murshudov, ActaD, 2013, and tell them to join us in 
the 21st century.





On 14/08/2013 16:41, Jeffrey, Philip D. wrote:

Hello Yafang,

The answer lies in the fact that you used HKL2000.  Scalepack has a 
long standing feature where it reports Rmerge  100% as zero.  Quite 
why they do that is a mystery, but your Rmerge in the outermost shell 
is NOT zero - the Rmerge for the lower resolution shells will show up 
as non-zero if Rmerge  100%.


That feature is overdue for a fix.

Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and 
import into CCP4 via Pointless and have Scala or Aimless report the 
correct statistics.  Reprocessing the data using XDS or Mosflm will 
ultimately lead you to scaling the data with a program that doesn't 
have that bug.  If you do this, report Rmeas rather than Rmerge, the 
former being a better measure.


Phil Jeffrey
Princeton



*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 
Yafang Chen [yafangche...@gmail.com]

*Sent:* Wednesday, August 14, 2013 11:32 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Rmerge of the last shell is zero

Dear All,

Here are some more details about the question I asked earlier about 
Rmerge is 0 in the last shell. I processed the data using HKL2000. 
The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 
(2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last 
shell, I preferred not to cut back the resolution any more. But I 
don't know how to explain Rmerge in the last shell being 0. Besides, I 
am wondering if this data is publishable (with Rmerge being 0 in the 
last shell). Thank you so much for your help!


Best,
Yafang


On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com 
mailto:yafangche...@gmail.com wrote:


Dear All,

I recently processed a dataset, in which I/sigmaI of the last
shell is 2.3, while Rmerge of the last shell is 0. Does anyone
know why the Rmerge is 0? The completeness is 100 (100). Thank you
so much for your help in advance!

Best,
Yafang

-- 
Yafang Chen

Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907




--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907




Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Edward A. Berry
But it is highly unlikely that sum(I) in the denominator is zero if I/sig(I) is 2 as reported (providing the sig(I) is 
valid- what was chi^2 in the last shell and overall?).


I sort of disagree that R-merge values over 1.0 are meaningless, provided not too far over. Granted R-meas is more 
meaningful, but with high redundancy R-merge approximates R-meas, and R-merge is what the PDB is accepting now.  A value 
a little over 1 tells you the standard deviation of the individual mesurements is a little larger than the average 
signal in those measurements. Understanding a little about distribution of intensities and error propogation (standard 
error of the mean, R-pim) the user will understand that quite a few reflections were stronger than this standard 
deviation, and that the error in the averaged intensities is be less than this standard deviation, and not have a 
problem. The problem comes with the 100%-sum mentality which says that if your error is 100% the signal must be zero%. 
That is why I don't like to express R-whatever as a percent. If the signal was really zero, R-merge or R-meas would be 
plus/minus infinity. So much for 100%-sum.


So rerun scalepack with no merge original index, reprocess through CCp4 or just rune Diedrich's rmerge program or 
phenix.merging_statistics to get the value of r-merge (and r-meas and R-pim and cc1/2) from the .sca file. If it is much 
over 3 than I would rexamine the I/sig(I) value (which can be misestimated) and consider discarding the last shell. If 
it is 3 or less, report it. The PDB ADDIT2 application used to not accept values over .99, but you can put that and ask 
the friendly annotator to correct it in the final PDB file. If the annotator objects, THEN point (him) to the 2012 KD 
paper- R-meas in the last shell there was over 4, and they concluded there was useful information.


Of course by then you will have refined your structure, and unbiased R-free in the last shell can be a good indicator. 
If you refine once in phenix you can use phenix.cc_star to calculate cc* and compare with R and R-free; from the output 
mtz file and your unmerged .sca file.

eab

Frank von Delft wrote:

This HKL2000 (scalepack) feature is actually extremely sensible:  an Rmerge 
that high is mathematically meaningless, it
quite literally tells you nothing at all about he signal in your data.

So I second James's advice:  just put n/a in your table 1.

If the reviewer complains, point them to Karplus  Diederichs, Science, 2012, 
and Evans and Murshudov, ActaD, 2013, and
tell them to join us in the 21st century.




On 14/08/2013 16:41, Jeffrey, Philip D. wrote:

Hello Yafang,

The answer lies in the fact that you used HKL2000.  Scalepack has a long standing 
feature where it reports Rmerge 
100% as zero.  Quite why they do that is a mystery, but your Rmerge in the 
outermost shell is NOT zero - the Rmerge
for the lower resolution shells will show up as non-zero if Rmerge  100%.

That feature is overdue for a fix.

Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import 
into CCP4 via Pointless and have Scala
or Aimless report the correct statistics.  Reprocessing the data using XDS or 
Mosflm will ultimately lead you to
scaling the data with a program that doesn't have that bug.  If you do this, 
report Rmeas rather than Rmerge, the
former being a better measure.

Phil Jeffrey
Princeton



*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen 
[yafangche...@gmail.com]
*Sent:* Wednesday, August 14, 2013 11:32 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Rmerge of the last shell is zero

Dear All,

Here are some more details about the question I asked earlier about Rmerge is 0 in 
the last shell. I processed the
data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma 
is 34.8 (2.3). Rmerge is 6.5 (0.0).
Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back 
the resolution any more. But I don't know
how to explain Rmerge in the last shell being 0. Besides, I am wondering if 
this data is publishable (with Rmerge
being 0 in the last shell). Thank you so much for your help!

Best,
Yafang


On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com 
mailto:yafangche...@gmail.com wrote:

Dear All,

I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, 
while Rmerge of the last shell is 0.
Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank 
you so much for your help in advance!

Best,
Yafang

--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907




--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department 

Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Nat Echols
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.eduwrote:

 If you refine once in phenix you can use phenix.cc_star to calculate cc*
 and compare with R and R-free; from the output mtz file and your unmerged
 .sca file.


FYI, this should also work with structures refined in Refmac, assuming it
can recalculate the R-factors to within a reasonable margin of error.

-Nat