Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Deepthi,

is it just a typo, or do your last two sentences say that your data DO
NOT scale in P312 but scale well in P321?

Did you try pointless for space group determination? I have not used
molrep for this purpose and cannot judge how reliable the self rotation
function is for space group determination.

Depending on your resolution and cell dimensions you may have very few
reflection for determining the screw axis.

Do your data suffer from radiation damage, does the cell become greater
during integration? Did you fix the detector distance during integration?

Best wishes,

Tim

On 04/04/12 23:07, Deepthi wrote:
 Hello everyone
 I have a problem scaling the MAD data which was collected a week ago.The
 data was collected at 1.5A resolution using three wavelengths for Zn-MAD
 experiments. Scaling the data for MAD experiments, the number of rejections
 and chi2 values were very high even after adjusting the error-scale factor
 and error model. The space group i used was p312 which i obtained by
 running a self-rotation function in MOLREP. When i scale my data using p312
 spacegroup the chi2 and rejections were huge. But he data was scaling well
 in p321 spacegroup. can anyone explain whats going on?
 
 Thank you very much
 
 Deepthi
 

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

GPG Key ID = A46BEE1A

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Re: [ccp4bb] Who is using 64-bit Linux?

2012-04-05 Thread Harry Powell

Hi David

I'm curious - do you mean running on a 32-bit Centos box or running  
the 32-bit Mosflm executable on a 64-bit Centos box?


We did have one report of problems with the 32-bit exe on a 64-bit  
box, which (seemingly) randomly gave one of two different results  
(either the same failure or success) - but that was fixed in the beta  
we released in July last year, and didn't occur with the 64-bit exe  
at all.


We really are grateful to people who tell us about the bugs they find  
rather than try to struggle on in silence!




Funny enough I can't get iMosflm running reliably on 32 bit CentOS  
5 or CentOS 6 and I can on 64 bits versions.


We have all running (CCP4, Coot, iMosflm, XDS, phenix, best, etc,  
etc) running in 64 bit and intent to move all user computers to  
uniform 64 bit environment on the next shutdown as it is more  
difficult to support both 32 and 64 bit enviroment.


David
--
David Aragao, PhD | Research Fellow - MX | Australian Synchrotron
p: (03) 8540 4121 | f: (03) 8540 4200 | m: 0467 775 203
david.ara...@synchrotron.org.au | www.synchrotron.org.au
800 Blackburn Road, Clayton, Victoria 3168, Australia


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Clemens Vonrhein
Hi,

On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote:
 Hello everyone
 I have a problem scaling the MAD data which was collected a week ago.The
 data was collected at 1.5A resolution using three wavelengths for Zn-MAD
 experiments. Scaling the data for MAD experiments, the number of rejections
 and chi2 values were very high even after adjusting the error-scale factor
 and error model. The space group i used was p312 which i obtained by
 running a self-rotation function in MOLREP. When i scale my data using p312
 spacegroup the chi2 and rejections were huge. But he data was scaling well
 in p321 spacegroup. can anyone explain whats going on?

When you say 'Scaling the data for MAD experiments': do you mean
scaling the various scans for your 3-wvl MAD data in a single scaling
job? Unless you already took care of this during data integration,
remember that your separate scans could have been indexed differently
and therefore don't match up. See eg.

  http://www.ccp4.ac.uk/html/reindexing.html

for some lookup-tables in P312 and P321. You can use the CCP4 program
'reindex' on MTZ files if needed.

But I guess most modern data-processing and scaling programs will take
care of that automatically anyway?

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***


Re: [ccp4bb] arp_waters still available?

2012-04-05 Thread Victor Lamzin

Dear Bernard,

arp_waters is a very old code and it gets even older as we speak.

Try to use ARP/wARP version 7.2, where you can run the same task:
from the command line ($warpbin/auto_solvent.sh)
from the CCP4i GUI (ARP/wARP Solvent)
from ArpNavigator (Model Solvent)

There should be both 32 and 64-bit versions.

Best regards,
Victor


On 05/04/2012 05:23, Bernhard Rupp (Hofkristallrat a.D.) wrote:

Dear Developers,

in some older scripts I still call the ccp4 version of arp_waters, which
worked well for dummy atom picking.
It does not seem to be included in recent 64 bit CCP4 packages. Does anyone
perhaps have
a precompiled 64 bit version of arp_waters that might run on RHEL62?

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-

No animals were hurt or killed during the
production of this email.
-


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread John R Helliwell
Dear 'aales...@burnham.org',

Re the pixel detector; yes this is an acknowledged raw data archiving
challenge; possible technical solutions include:- summing to make
coarser images ie in angular range, lossless compression (nicely
described on this CCP4bb by James Holton) or preserving a sufficient
sample of data(but nb this debate is certainly not yet concluded).

Re And all this hassle is for the only real purpose of preventing data fraud?

Well.Why publish data?
Please let me offer some reasons:
• To enhance the reproducibility of a scientific experiment
• To verify or support the validity of deductions from an experiment
• To safeguard against error
• To allow other scholars to conduct further research based on
experiments already conducted
• To allow reanalysis at a later date, especially to extract 'new'
science as new techniques are developed
• To provide example materials for teaching and learning
• To provide long-term preservation of experimental results and future
access to them
• To permit systematic collection for comparative studies
• And, yes, To better safeguard against fraud than is apparently the
case at present

Also to (probably) comply with your funding agency's grant conditions:-
Increasingly, funding agencies are requesting or requiring data
management policies (including provision for retention and access) to
be taken into account when awarding grants. See e.g. the Research
Councils UK Common Principles on Data Policy
(http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
Curation Centre overview of funding policies in the UK
(http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies).
See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
on policies relevant to crystallography in other countries. Nb these
policies extend over derived, processed and raw data, ie without
really an adequate clarity of policy from one to the other stages of
the 'data pyramid' ((see
http://www.stm-assoc.org/integration-of-data-and-publications).


And just to mention IUCr Journals Notes for Authors for biological
macromolecular structures, where we have our ie macromolecular
crystallography's version of the 'data pyramid' :-

(1) Derived data
• Atomic coordinates, anisotropic or isotropic displacement
parameters, space group information, secondary structure and
information about biological functionality must be deposited with the
Protein Data Bank before or in concert with article publication; the
article will link to the PDB deposition using the PDB reference code.
• Relevant experimental parameters, unit-cell dimensions are required
as an integral part of article submission and are published within the
article.

(2) Processed experimental data
• Structure factors must be deposited with the Protein Data Bank
before or in concert with article publication; the article will link
to the PDB deposition using the PDB reference code.

(3) Primary experimental data (here I give small and macromolecule
Notes for Authors details):-
For small-unit-cell crystal/molecular structures and macromolecular
structures IUCr journals have no current binding policy regarding
publication of diffraction images or similar raw data entities.
However, the journals welcome efforts made to preserve and provide
primary experimental data sets. Authors are encouraged to make
arrangements for the diffraction data images for their structure to be
archived and available on request.
For articles that present the results of powder diffraction profile
fitting or refinement (Rietveld) methods, the primary diffraction
data, i.e. the numerical intensity of each measured point on the
profile as a function of scattering angle, should be deposited.
Fibre data should contain appropriate information such as a photograph
of the data. As primary diffraction data cannot be satisfactorily
extracted from such figures, the basic digital diffraction data should
be deposited.


Finally to mention that many IUCr Commissions are interested in the
possibility of establishing community practices for the orderly
retention and referencing of raw data sets, and the IUCr would like to
see such data sets become part of the routine record of scientific
research in the future, to the extent that this proves feasible and
cost-effective.
I draw your attention therefore to the IUCr Forum on such matters at:-
http://forums.iucr.org/
Within this Forum you can find for example the ICSU convened Strategic
Coordinating Committee on Information and Data fairly recent report;
within this we learn of many other areas of science efforts on data
archiving and eg that the radio astronomy square kilometre array will
pose the biggest raw data archiving challenge on the planet.[Our needs
are thereby relatively modest.]

The IUCr Diffraction Data Deposition Working Group is actively
addressing all these various issues.
We weclome your input at the IUCr Forum, which will thereby be most
timely. Thankyou.

Best wishes,
Yours 

[ccp4bb] CCP-EM positions now available

2012-04-05 Thread Gerard DVD Kleywegt

[Cross-posted from the 3DEM mailing list.]

--Gerard

-- Forwarded message --
Date: Wed, 4 Apr 2012 16:34:39 +0100
From: Helen Saibil h.sai...@mail.cryst.bbk.ac.uk
To: 3DEM Mailing List 3...@ncmir.ucsd.edu
Subject: [3dem] CCP-EM positions now available

Dear Colleagues,

We have been awarded a Partnership grant by the MRC to provide computational 
support for UK scientists using electron cryo-microscopy for structural 
biology. One of the major aims is to create a Collaborative Computational 
Project, CCP-EM, by analogy with similar successful projects in macromolecular 
crystallography (CCP4) and biological nuclear magnetic resonance spectroscopy 
(CCPN). We seek two excellent and motivated computational scientists to 
support the Partnership grant and the CCP-EM project. These posts will have a 
wide variety of responsibilities, including writing community code, improving 
the useability of existing code, providing training, and supporting individual 
scientists. The first post will focus on technical aspects, building community 
tools and improving the programs available. The second post will focus more on 
the scientific requirements of the community. The posts are located at the 
Research Complex at Harwell, alongside the core group of CCP4, but the 
postholders will be expected to travel throughout the UK and interact with 
international groups to support the collaboration.


Applications must be made through the RCUK Shared Services recruitment portal 
https://ext.ssc.rcuk.ac.uk/ using the references IRC50385 and IRC50666. 
Informal enquiries may be made to Martyn Winn (martyn.w...@stfc.ac.uk).


Best wishes,

Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil 
and Ardan Patwardhan


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Herbert J. Bernstein

Dear Colleagues,

  Clearly, no system will be able to perfectly preserve every pixel of
every dataset collected at a cost that can be afforded.  Resources are
finite and we must set priorities.  I would suggest that, in order
of declining priority, we try our best to retain:

  1.  raw data that might tend to refute published results
  2.  raw data that might tend to support published results
  3.  raw data that may be of significant use in currently
ongoing studies either in refutation or support
  4.  raw data that may be of significant use in future
studies

While no archiving system can be perfect, we should not let the
search for a perfect solution prevent us from working with
currently available good solutions, and even in this era of tight
budgets, there are good solutions.

  Regards,
Herbert

On 4/5/12 7:16 AM, John R Helliwell wrote:

Dear 'aales...@burnham.org',

Re the pixel detector; yes this is an acknowledged raw data archiving
challenge; possible technical solutions include:- summing to make
coarser images ie in angular range, lossless compression (nicely
described on this CCP4bb by James Holton) or preserving a sufficient
sample of data(but nb this debate is certainly not yet concluded).

Re And all this hassle is for the only real purpose of preventing data fraud?

Well.Why publish data?
Please let me offer some reasons:
• To enhance the reproducibility of a scientific experiment
• To verify or support the validity of deductions from an experiment
• To safeguard against error
• To allow other scholars to conduct further research based on
experiments already conducted
• To allow reanalysis at a later date, especially to extract 'new'
science as new techniques are developed
• To provide example materials for teaching and learning
• To provide long-term preservation of experimental results and future
access to them
• To permit systematic collection for comparative studies
• And, yes, To better safeguard against fraud than is apparently the
case at present

Also to (probably) comply with your funding agency's grant conditions:-
Increasingly, funding agencies are requesting or requiring data
management policies (including provision for retention and access) to
be taken into account when awarding grants. See e.g. the Research
Councils UK Common Principles on Data Policy
(http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
Curation Centre overview of funding policies in the UK
(http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies).
See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
on policies relevant to crystallography in other countries. Nb these
policies extend over derived, processed and raw data, ie without
really an adequate clarity of policy from one to the other stages of
the 'data pyramid' ((see
http://www.stm-assoc.org/integration-of-data-and-publications).


And just to mention IUCr Journals Notes for Authors for biological
macromolecular structures, where we have our ie macromolecular
crystallography's version of the 'data pyramid' :-

(1) Derived data
• Atomic coordinates, anisotropic or isotropic displacement
parameters, space group information, secondary structure and
information about biological functionality must be deposited with the
Protein Data Bank before or in concert with article publication; the
article will link to the PDB deposition using the PDB reference code.
• Relevant experimental parameters, unit-cell dimensions are required
as an integral part of article submission and are published within the
article.

(2) Processed experimental data
• Structure factors must be deposited with the Protein Data Bank
before or in concert with article publication; the article will link
to the PDB deposition using the PDB reference code.

(3) Primary experimental data (here I give small and macromolecule
Notes for Authors details):-
For small-unit-cell crystal/molecular structures and macromolecular
structures IUCr journals have no current binding policy regarding
publication of diffraction images or similar raw data entities.
However, the journals welcome efforts made to preserve and provide
primary experimental data sets. Authors are encouraged to make
arrangements for the diffraction data images for their structure to be
archived and available on request.
For articles that present the results of powder diffraction profile
fitting or refinement (Rietveld) methods, the primary diffraction
data, i.e. the numerical intensity of each measured point on the
profile as a function of scattering angle, should be deposited.
Fibre data should contain appropriate information such as a photograph
of the data. As primary diffraction data cannot be satisfactorily
extracted from such figures, the basic digital diffraction data should
be deposited.


Finally to mention that many IUCr Commissions are interested in the
possibility of establishing community practices for the orderly
retention and referencing of raw data 

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Roger Rowlett
FYI, every NSF grant proposal now must have a data management plan that
describes how all experimental data will be archived and in what formats.
I'm not sure how seriously these plans are monitored, but a plan must be
provided nevertheless. Is anyone NOT archiving their original data in some
way?

Roger Rowlett
On Apr 5, 2012 7:16 AM, John R Helliwell jrhelliw...@gmail.com wrote:

 Dear 'aales...@burnham.org',

 Re the pixel detector; yes this is an acknowledged raw data archiving
 challenge; possible technical solutions include:- summing to make
 coarser images ie in angular range, lossless compression (nicely
 described on this CCP4bb by James Holton) or preserving a sufficient
 sample of data(but nb this debate is certainly not yet concluded).

 Re And all this hassle is for the only real purpose of preventing data
 fraud?

 Well.Why publish data?
 Please let me offer some reasons:
 • To enhance the reproducibility of a scientific experiment
 • To verify or support the validity of deductions from an experiment
 • To safeguard against error
 • To allow other scholars to conduct further research based on
 experiments already conducted
 • To allow reanalysis at a later date, especially to extract 'new'
 science as new techniques are developed
 • To provide example materials for teaching and learning
 • To provide long-term preservation of experimental results and future
 access to them
 • To permit systematic collection for comparative studies
 • And, yes, To better safeguard against fraud than is apparently the
 case at present

 Also to (probably) comply with your funding agency's grant conditions:-
 Increasingly, funding agencies are requesting or requiring data
 management policies (including provision for retention and access) to
 be taken into account when awarding grants. See e.g. the Research
 Councils UK Common Principles on Data Policy
 (http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
 Curation Centre overview of funding policies in the UK
 (
 http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies
 ).
 See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
 on policies relevant to crystallography in other countries. Nb these
 policies extend over derived, processed and raw data, ie without
 really an adequate clarity of policy from one to the other stages of
 the 'data pyramid' ((see
 http://www.stm-assoc.org/integration-of-data-and-publications).


 And just to mention IUCr Journals Notes for Authors for biological
 macromolecular structures, where we have our ie macromolecular
 crystallography's version of the 'data pyramid' :-

 (1) Derived data
 • Atomic coordinates, anisotropic or isotropic displacement
 parameters, space group information, secondary structure and
 information about biological functionality must be deposited with the
 Protein Data Bank before or in concert with article publication; the
 article will link to the PDB deposition using the PDB reference code.
 • Relevant experimental parameters, unit-cell dimensions are required
 as an integral part of article submission and are published within the
 article.

 (2) Processed experimental data
 • Structure factors must be deposited with the Protein Data Bank
 before or in concert with article publication; the article will link
 to the PDB deposition using the PDB reference code.

 (3) Primary experimental data (here I give small and macromolecule
 Notes for Authors details):-
 For small-unit-cell crystal/molecular structures and macromolecular
 structures IUCr journals have no current binding policy regarding
 publication of diffraction images or similar raw data entities.
 However, the journals welcome efforts made to preserve and provide
 primary experimental data sets. Authors are encouraged to make
 arrangements for the diffraction data images for their structure to be
 archived and available on request.
 For articles that present the results of powder diffraction profile
 fitting or refinement (Rietveld) methods, the primary diffraction
 data, i.e. the numerical intensity of each measured point on the
 profile as a function of scattering angle, should be deposited.
 Fibre data should contain appropriate information such as a photograph
 of the data. As primary diffraction data cannot be satisfactorily
 extracted from such figures, the basic digital diffraction data should
 be deposited.


 Finally to mention that many IUCr Commissions are interested in the
 possibility of establishing community practices for the orderly
 retention and referencing of raw data sets, and the IUCr would like to
 see such data sets become part of the routine record of scientific
 research in the future, to the extent that this proves feasible and
 cost-effective.
 I draw your attention therefore to the IUCr Forum on such matters at:-
 http://forums.iucr.org/
 Within this Forum you can find for example the ICSU convened Strategic
 Coordinating Committee on Information and Data 

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bosch, Juergen
I would say everybody keeps probably too many junk datasets around - at least I 
do. And I run into the trouble of having to buy new TB plates every now and 
then.
I think on average per year my group acquires currently ~700 GB of raw images 
(compressed), now if we were to only keep the useful datasets we probably would 
be down to 10% of that. But as always you hope for the best and keep some data 
considered junk in 2009 which might be useful in 2015.

Jürgen

On Apr 5, 2012, at 9:08 AM, Roger Rowlett wrote:


FYI, every NSF grant proposal now must have a data management plan that 
describes how all experimental data will be archived and in what formats. I'm 
not sure how seriously these plans are monitored, but a plan must be provided 
nevertheless. Is anyone NOT archiving their original data in some way?

Roger Rowlett

On Apr 5, 2012 7:16 AM, John R Helliwell 
jrhelliw...@gmail.commailto:jrhelliw...@gmail.com wrote:
Dear 'aales...@burnham.orgmailto:aales...@burnham.org',

Re the pixel detector; yes this is an acknowledged raw data archiving
challenge; possible technical solutions include:- summing to make
coarser images ie in angular range, lossless compression (nicely
described on this CCP4bb by James Holton) or preserving a sufficient
sample of data(but nb this debate is certainly not yet concluded).

Re And all this hassle is for the only real purpose of preventing data fraud?

Well.Why publish data?
Please let me offer some reasons:
• To enhance the reproducibility of a scientific experiment
• To verify or support the validity of deductions from an experiment
• To safeguard against error
• To allow other scholars to conduct further research based on
experiments already conducted
• To allow reanalysis at a later date, especially to extract 'new'
science as new techniques are developed
• To provide example materials for teaching and learning
• To provide long-term preservation of experimental results and future
access to them
• To permit systematic collection for comparative studies
• And, yes, To better safeguard against fraud than is apparently the
case at present

Also to (probably) comply with your funding agency's grant conditions:-
Increasingly, funding agencies are requesting or requiring data
management policies (including provision for retention and access) to
be taken into account when awarding grants. See e.g. the Research
Councils UK Common Principles on Data Policy
(http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
Curation Centre overview of funding policies in the UK
(http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies).
See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
on policies relevant to crystallography in other countries. Nb these
policies extend over derived, processed and raw data, ie without
really an adequate clarity of policy from one to the other stages of
the 'data pyramid' ((see
http://www.stm-assoc.org/integration-of-data-and-publications).


And just to mention IUCr Journals Notes for Authors for biological
macromolecular structures, where we have our ie macromolecular
crystallography's version of the 'data pyramid' :-

(1) Derived data
• Atomic coordinates, anisotropic or isotropic displacement
parameters, space group information, secondary structure and
information about biological functionality must be deposited with the
Protein Data Bank before or in concert with article publication; the
article will link to the PDB deposition using the PDB reference code.
• Relevant experimental parameters, unit-cell dimensions are required
as an integral part of article submission and are published within the
article.

(2) Processed experimental data
• Structure factors must be deposited with the Protein Data Bank
before or in concert with article publication; the article will link
to the PDB deposition using the PDB reference code.

(3) Primary experimental data (here I give small and macromolecule
Notes for Authors details):-
For small-unit-cell crystal/molecular structures and macromolecular
structures IUCr journals have no current binding policy regarding
publication of diffraction images or similar raw data entities.
However, the journals welcome efforts made to preserve and provide
primary experimental data sets. Authors are encouraged to make
arrangements for the diffraction data images for their structure to be
archived and available on request.
For articles that present the results of powder diffraction profile
fitting or refinement (Rietveld) methods, the primary diffraction
data, i.e. the numerical intensity of each measured point on the
profile as a function of scattering angle, should be deposited.
Fibre data should contain appropriate information such as a photograph
of the data. As primary diffraction data cannot be satisfactorily
extracted from such figures, the basic digital diffraction data should
be deposited.


Finally to mention that many IUCr Commissions are interested in the

[ccp4bb] Category 4 Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Jrh
Dear Herbert,
Category 4, in Manchester, we find is tricky, for want of a better word. 
Needless to say that we have collaborators on our Crystallography Research 
Service who request data sets from eg ten years ago, that are now urgent for 
publication writing up. So we are keeping everything, although only recent 
years the raw diffraction images, and nb soon to be assisted by the Univ 
Manchester centralised Data Repository for its researchers. (Incidentally I 
have kept all of my film oscillation, and inc later Laue data, back to approx 
1977, which fills a whole wall shelf worth, ~ 10 metres.)
Greetings,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 5 Apr 2012, at 13:50, Herbert J. Bernstein y...@bernstein-plus-sons.com 
wrote:

 Dear Colleagues,
 
  Clearly, no system will be able to perfectly preserve every pixel of
 every dataset collected at a cost that can be afforded.  Resources are
 finite and we must set priorities.  I would suggest that, in order
 of declining priority, we try our best to retain:
 
  1.  raw data that might tend to refute published results
  2.  raw data that might tend to support published results
  3.  raw data that may be of significant use in currently
 ongoing studies either in refutation or support
  4.  raw data that may be of significant use in future
 studies
 
 While no archiving system can be perfect, we should not let the
 search for a perfect solution prevent us from working with
 currently available good solutions, and even in this era of tight
 budgets, there are good solutions.
 
  Regards,
Herbert
 
 On 4/5/12 7:16 AM, John R Helliwell wrote:
 Dear 'aales...@burnham.org',
 
 Re the pixel detector; yes this is an acknowledged raw data archiving
 challenge; possible technical solutions include:- summing to make
 coarser images ie in angular range, lossless compression (nicely
 described on this CCP4bb by James Holton) or preserving a sufficient
 sample of data(but nb this debate is certainly not yet concluded).
 
 Re And all this hassle is for the only real purpose of preventing data 
 fraud?
 
 Well.Why publish data?
 Please let me offer some reasons:
 • To enhance the reproducibility of a scientific experiment
 • To verify or support the validity of deductions from an experiment
 • To safeguard against error
 • To allow other scholars to conduct further research based on
 experiments already conducted
 • To allow reanalysis at a later date, especially to extract 'new'
 science as new techniques are developed
 • To provide example materials for teaching and learning
 • To provide long-term preservation of experimental results and future
 access to them
 • To permit systematic collection for comparative studies
 • And, yes, To better safeguard against fraud than is apparently the
 case at present
 
 Also to (probably) comply with your funding agency's grant conditions:-
 Increasingly, funding agencies are requesting or requiring data
 management policies (including provision for retention and access) to
 be taken into account when awarding grants. See e.g. the Research
 Councils UK Common Principles on Data Policy
 (http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
 Curation Centre overview of funding policies in the UK
 (http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies).
 See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
 on policies relevant to crystallography in other countries. Nb these
 policies extend over derived, processed and raw data, ie without
 really an adequate clarity of policy from one to the other stages of
 the 'data pyramid' ((see
 http://www.stm-assoc.org/integration-of-data-and-publications).
 
 
 And just to mention IUCr Journals Notes for Authors for biological
 macromolecular structures, where we have our ie macromolecular
 crystallography's version of the 'data pyramid' :-
 
 (1) Derived data
 • Atomic coordinates, anisotropic or isotropic displacement
 parameters, space group information, secondary structure and
 information about biological functionality must be deposited with the
 Protein Data Bank before or in concert with article publication; the
 article will link to the PDB deposition using the PDB reference code.
 • Relevant experimental parameters, unit-cell dimensions are required
 as an integral part of article submission and are published within the
 article.
 
 (2) Processed experimental data
 • Structure factors must be deposited with the Protein Data Bank
 before or in concert with article publication; the article will link
 to the PDB deposition using the PDB reference code.
 
 (3) Primary experimental data (here I give small and macromolecule
 Notes for Authors details):-
 For small-unit-cell crystal/molecular structures and macromolecular
 structures IUCr journals have no 

[ccp4bb] Via Annual Reports...Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Jrh
Dear Roger,
At the recent ICSTI Workshop on Delivering Data in science the NSF presenter, 
when I asked about monitoring, replied that the PIs' annual reports should 
include data management aspects.
See http://www.icsti.org/spip.php?rubrique42
Best wishes,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 5 Apr 2012, at 14:08, Roger Rowlett rrowl...@colgate.edu wrote:

 FYI, every NSF grant proposal now must have a data management plan that 
 describes how all experimental data will be archived and in what formats. I'm 
 not sure how seriously these plans are monitored, but a plan must be provided 
 nevertheless. Is anyone NOT archiving their original data in some way?
 
 Roger Rowlett
 
 On Apr 5, 2012 7:16 AM, John R Helliwell jrhelliw...@gmail.com wrote:
 Dear 'aales...@burnham.org',
 
 Re the pixel detector; yes this is an acknowledged raw data archiving
 challenge; possible technical solutions include:- summing to make
 coarser images ie in angular range, lossless compression (nicely
 described on this CCP4bb by James Holton) or preserving a sufficient
 sample of data(but nb this debate is certainly not yet concluded).
 
 Re And all this hassle is for the only real purpose of preventing data 
 fraud?
 
 Well.Why publish data?
 Please let me offer some reasons:
 • To enhance the reproducibility of a scientific experiment
 • To verify or support the validity of deductions from an experiment
 • To safeguard against error
 • To allow other scholars to conduct further research based on
 experiments already conducted
 • To allow reanalysis at a later date, especially to extract 'new'
 science as new techniques are developed
 • To provide example materials for teaching and learning
 • To provide long-term preservation of experimental results and future
 access to them
 • To permit systematic collection for comparative studies
 • And, yes, To better safeguard against fraud than is apparently the
 case at present
 
 Also to (probably) comply with your funding agency's grant conditions:-
 Increasingly, funding agencies are requesting or requiring data
 management policies (including provision for retention and access) to
 be taken into account when awarding grants. See e.g. the Research
 Councils UK Common Principles on Data Policy
 (http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx) and the Digital
 Curation Centre overview of funding policies in the UK
 (http://www.dcc.ac.uk/resources/policy-and-legal/overview-funders-data-policies).
 See also http://forums.iucr.org/viewtopic.php?f=21t=58 for discussion
 on policies relevant to crystallography in other countries. Nb these
 policies extend over derived, processed and raw data, ie without
 really an adequate clarity of policy from one to the other stages of
 the 'data pyramid' ((see
 http://www.stm-assoc.org/integration-of-data-and-publications).
 
 
 And just to mention IUCr Journals Notes for Authors for biological
 macromolecular structures, where we have our ie macromolecular
 crystallography's version of the 'data pyramid' :-
 
 (1) Derived data
 • Atomic coordinates, anisotropic or isotropic displacement
 parameters, space group information, secondary structure and
 information about biological functionality must be deposited with the
 Protein Data Bank before or in concert with article publication; the
 article will link to the PDB deposition using the PDB reference code.
 • Relevant experimental parameters, unit-cell dimensions are required
 as an integral part of article submission and are published within the
 article.
 
 (2) Processed experimental data
 • Structure factors must be deposited with the Protein Data Bank
 before or in concert with article publication; the article will link
 to the PDB deposition using the PDB reference code.
 
 (3) Primary experimental data (here I give small and macromolecule
 Notes for Authors details):-
 For small-unit-cell crystal/molecular structures and macromolecular
 structures IUCr journals have no current binding policy regarding
 publication of diffraction images or similar raw data entities.
 However, the journals welcome efforts made to preserve and provide
 primary experimental data sets. Authors are encouraged to make
 arrangements for the diffraction data images for their structure to be
 archived and available on request.
 For articles that present the results of powder diffraction profile
 fitting or refinement (Rietveld) methods, the primary diffraction
 data, i.e. the numerical intensity of each measured point on the
 profile as a function of scattering angle, should be deposited.
 Fibre data should contain appropriate information such as a photograph
 of the data. As primary diffraction data cannot be satisfactorily
 extracted from such figures, the basic digital diffraction data should
 be deposited.
 
 
 Finally to mention that 

[ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Francis E Reyes
It seems that deposition of map coefficients is a good idea. Does someone have 
an mtz2cif that can handle this? 

Thanks!

F





-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder


Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Pete Meyer

Have you tried mtz2various (with cif output)?

Pete

Francis E Reyes wrote:
It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? 


Thanks!

F





-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder


Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote:
 It seems that deposition of map coefficients is a good idea. 
 Does someone have an mtz2cif that can handle this? 

Maybe I missed something.
What is accomplished by depositing map coefficients that isn't
done better by depositing Fo and Fc?

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742


Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Miller, Mitchell D.
I have not tried it, but the latest version of the rcsb 
program sf-convert is supposed to support it 
(see version 1.2 released March 23)
http://sw-tools.pdb.org/apps/SF-CONVERT/index.html
http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-2-00/documentation.html
(Version 1.2 is not yet available as a binary download)
Regards,
Mitch


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Francis E 
Reyes
Sent: Thursday, April 05, 2012 8:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mtz2cif capable of handling map coefficients

It seems that deposition of map coefficients is a good idea. Does someone have 
an mtz2cif that can handle this? 

Thanks!

F





-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder


Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Phil Jeffrey
Fc doesn't contain the weighting scheme used in the creation of the map 
coefficients, so Fc would require some sort of program to be run to 
recreate those for both 2Fo-Fc and Fo-Fc maps. By which time you might 
as well run a single cycle of the refinement program in question to 
generate new map coefficients - so I don't see the benefit of Fc.


The map coefficients, on the other hand, are a checkpoint of the maps 
being looked at by the author at the time of deposition and don't 
require programs beyond a typical visualization program (i.e. Coot) to view.


Phil Jeffrey
Princeton

On 4/5/12 12:00 PM, Ethan Merritt wrote:

On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote:

It seems that deposition of map coefficients is a good idea.
Does someone have an mtz2cif that can handle this?


Maybe I missed something.
What is accomplished by depositing map coefficients that isn't
done better by depositing Fo and Fc?

Ethan



Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Deepthi
Hello

I arrived at the p312 space group by running a self rotation function using
MOLREP. The maps show the space group as p312. I was scaling the data
individually for each wavelength. None of the three wavelengths are scaling
are scaling in p312 space group.

On Thu, Apr 5, 2012 at 2:17 AM, Clemens Vonrhein vonrh...@globalphasing.com
 wrote:

 Hi,

 On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote:
  Hello everyone
  I have a problem scaling the MAD data which was collected a week ago.The
  data was collected at 1.5A resolution using three wavelengths for Zn-MAD
  experiments. Scaling the data for MAD experiments, the number of
 rejections
  and chi2 values were very high even after adjusting the error-scale
 factor
  and error model. The space group i used was p312 which i obtained by
  running a self-rotation function in MOLREP. When i scale my data using
 p312
  spacegroup the chi2 and rejections were huge. But he data was scaling
 well
  in p321 spacegroup. can anyone explain whats going on?

 When you say 'Scaling the data for MAD experiments': do you mean
 scaling the various scans for your 3-wvl MAD data in a single scaling
 job? Unless you already took care of this during data integration,
 remember that your separate scans could have been indexed differently
 and therefore don't match up. See eg.

  http://www.ccp4.ac.uk/html/reindexing.html

 for some lookup-tables in P312 and P321. You can use the CCP4 program
 'reindex' on MTZ files if needed.

 But I guess most modern data-processing and scaling programs will take
 care of that automatically anyway?

 Cheers

 Clemens

 --

 ***
 * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
 *
 *  Global Phasing Ltd.
 *  Sheraton House, Castle Park
 *  Cambridge CB3 0AX, UK
 *--
 * BUSTER Development Group  (http://www.globalphasing.com)
 ***




-- 
Deepthi


Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Matthew Franklin

Hi -

Let me just add that P312 is a very uncommon space group for protein 
crystals, much less common than P321.  (This doesn't mean you don't have 
it - it's just unlikely.)  If you look at PDB statistics:


P 3 1 2 : 12 structures
P3(1) 1 2: 61 structures
P3(2) 1 2: 85 structures

P 3 2 1 : 278 structures
P3(1) 2 1: 2354 structures
P3(2) 2 1: 2533 structures

This also suggests, by the way, that you have a screw axis that you 
haven't accounted for yet.  It won't affect your data scaling, but it 
sure will affect your molecular replacement job!


Hope that helps,
Matt


On 4/5/12 12:31 PM, Deepthi wrote:

Hello

I arrived at the p312 space group by running a self rotation function 
using MOLREP. The maps show the space group as p312. I was scaling the 
data individually for each wavelength. None of the three wavelengths 
are scaling are scaling in p312 space group.


On Thu, Apr 5, 2012 at 2:17 AM, Clemens Vonrhein 
vonrh...@globalphasing.com mailto:vonrh...@globalphasing.com wrote:


Hi,

On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote:
 Hello everyone
 I have a problem scaling the MAD data which was collected a week
ago.The
 data was collected at 1.5A resolution using three wavelengths
for Zn-MAD
 experiments. Scaling the data for MAD experiments, the number of
rejections
 and chi2 values were very high even after adjusting the
error-scale factor
 and error model. The space group i used was p312 which i obtained by
 running a self-rotation function in MOLREP. When i scale my data
using p312
 spacegroup the chi2 and rejections were huge. But he data was
scaling well
 in p321 spacegroup. can anyone explain whats going on?

When you say 'Scaling the data for MAD experiments': do you mean
scaling the various scans for your 3-wvl MAD data in a single scaling
job? Unless you already took care of this during data integration,
remember that your separate scans could have been indexed differently
and therefore don't match up. See eg.

http://www.ccp4.ac.uk/html/reindexing.html

for some lookup-tables in P312 and P321. You can use the CCP4 program
'reindex' on MTZ files if needed.

But I guess most modern data-processing and scaling programs will take
care of that automatically anyway?

Cheers

Clemens

--

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***




--
Deepthi



--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165



Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote:
 Fc doesn't contain the weighting scheme used in the creation of the map 
 coefficients, so Fc would require some sort of program to be run to 
 recreate those for both 2Fo-Fc and Fo-Fc maps.  

The viewers I am familiar with do this for themselves on the fly.
No need to involve additional programs. In fact, generating and storing
map coefficients is not part of my work flow, since none of the programs 
I normally use need them to be pre-calculated.

 By which time you might 
 as well run a single cycle of the refinement program in question to 
 generate new map coefficients - so I don't see the benefit of Fc.

You must use a different tool set than I do.
 
 The map coefficients, on the other hand, are a checkpoint of the maps 
 being looked at by the author at the time of deposition and don't 
 require programs beyond a typical visualization program (i.e. Coot) to view.

But is that a good thing or a bad thing?

I would rather make my own call about weighting and choice of maps,
so I would rather have the Fo and Fc.  Anyhow, Coot reads in and displays
maps just fine from an mtz or cif file containing Fo and Fc but no
map coefficients.   It is true that usually you want to have a value for 
the FOM or other weight avalailable also.

cheers,

Ethan


 Phil Jeffrey
 Princeton
 
 On 4/5/12 12:00 PM, Ethan Merritt wrote:
  On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote:
  It seems that deposition of map coefficients is a good idea.
  Does someone have an mtz2cif that can handle this?
 
  Maybe I missed something.
  What is accomplished by depositing map coefficients that isn't
  done better by depositing Fo and Fc?
 
  Ethan
 
 
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742


Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Oliver Smart

On Thu, 5 Apr 2012, Ethan Merritt wrote:


On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote:

Fc doesn't contain the weighting scheme used in the creation of the map
coefficients, so Fc would require some sort of program to be run to
recreate those for both 2Fo-Fc and Fo-Fc maps.


The viewers I am familiar with do this for themselves on the fly.
No need to involve additional programs. In fact, generating and storing
map coefficients is not part of my work flow, since none of the programs
I normally use need them to be pre-calculated.




Ethan,

If you load a mtz file from refmac or BUSTER then this file contains Map 
Coefficients. Different programs and protocols produce different maps. So 
I second Phil's comment that including map coefficients in deposition is a 
really good thing. It will enable people to see exactly the maps as seen 
by the depositor (and to do so in a few years time). Hence we have 
included map coefficients in 3 recent depositions 3syu, 3urp, 3v56 (using 
a prototype mtz2cif tool that is not quite ready for release yet).


We have also worked out how to patch ccp4 cif2mtz so that it can do the 
reverse process see


https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112


Regards,

Oliver


[ccp4bb] PDF position Structural Cell Biology - Michigan

2012-04-05 Thread Amir Khan
Hi,
I would like to advertise a position on behalf of Prof. Lois Weisman 
((Michigan).
Interested parties should contact her directly 
(lweisman.off...@gmail.commailto:lweisman.off...@gmail.com).
-Amir

Postdoctoral Fellow Position
Integration of high resolution structures with biology
Seeking a highly motivated postdoctoral fellow to initiate a new project in the 
general areas of phosphoinositide signaling or myosin V-based transport. We are 
a highly multidisciplinary, interactive laboratory, and use diverse techniques 
to address cutting edge questions on the roles and regulation of PtdIns(3,5)P2 
and PtdIns(5)P in yeast and mice. Specifically we are determining how the lipid 
kinase, Fab1/PIKfyve is regulated, identifying the upstream signaling pathways, 
and downstream targets. In addition, we seek to determine the precise roles of 
Fab1/PIKfyve in the nervous system, and how minor perturbations in this pathway 
lead to profound neurodegeneration. Another critical area of research is 
determining how myosin V attaches to cargoes. We recently found that the 
cargo-binding domain of myosin V interacts directly with a subunit of the 
exocyst tethering complex [Jin et al. (2011) Dev. Cell. 21(6):1156-70.].  This 
paper illustrates the power of combining yeast genetics with high-resolution 
structures. Many additional projects in our lab are poised to utilize this type 
of approach.  For an overview of recent projects, see our website:
http://www.lsi.umich.edu/facultyresearch/labs/weisman

Qualifications: A Ph.D. in the life sciences. Experience in molecular, 
biochemical and/or cell biological techniques. A level of publications 
appropriate for the current level of training. The applicant should be 
dedicated to research in the life sciences and have a strong desire to make 
major contributions. Please submit cover letter, CV with name of three 
references, and a brief paragraph indicating a project of interest to 
lweisman.off...@gmail.commailto:lweisman.off...@gmail.com

The University of Michigan is an equal opportunity/affirmative action employer.



Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 10:48:16 am Oliver Smart wrote:
 
 On Thu, 5 Apr 2012, Ethan Merritt wrote:
 
  On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote:
  Fc doesn't contain the weighting scheme used in the creation of the map
  coefficients, so Fc would require some sort of program to be run to
  recreate those for both 2Fo-Fc and Fo-Fc maps.
 
  The viewers I am familiar with do this for themselves on the fly.
  No need to involve additional programs. In fact, generating and storing
  map coefficients is not part of my work flow, since none of the programs
  I normally use need them to be pre-calculated.
 
 
 
 Ethan,
 
 If you load a mtz file from refmac or BUSTER then this file contains Map 
 Coefficients. Different programs and protocols produce different maps.


I am bowing out of this discussion with apologies for any confusion that
I caused.  

I have realized that there may be a generational difference in
understanding the term map coefficient (or else my poor brain is just
not functioning as well as it ought to).  I thought that the proposal was
to require depositing the equivalent of a ccp4 *.map file, i.e. the 
real-space side of the Fourier transform.  I see now that people are
using map coefficient to mean weighted F, which was not what I originally
understood.

please carry on!

Ethan


 So 
 I second Phil's comment that including map coefficients in deposition is a 
 really good thing. It will enable people to see exactly the maps as seen 
 by the depositor (and to do so in a few years time). Hence we have 
 included map coefficients in 3 recent depositions 3syu, 3urp, 3v56 (using 
 a prototype mtz2cif tool that is not quite ready for release yet).
 
 We have also worked out how to patch ccp4 cif2mtz so that it can do the 
 reverse process see
 
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112
 
 
 Regards,
 
 Oliver
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Dear John,
Thank you for a very informative letter about the IUCr activities towards 
archiving the experimental data. I feel that I did not explain myself properly. 
I do not object archiving the raw data, I just believe that current methodology 
of validating data at PDB is insufficiently robust and requires a modification. 
Implementation of the raw image storage and validation will take a considerable 
time, while the recent incidents of a presumable data frauds demonstrate that 
the issue is urgent. Moreover, presenting the calculated structural factors in 
place of the experimental data is not the only abuse that the current 
validation procedure encourages to do. There might be more numerous occurances 
of data massaging like overestimation of the resolution or data quality, the 
system does not allow to verify them. IUCr and PDB follows the American 
taxation policy, where the responsibility for a fraud is placed on people, and 
the agency does not take sufficient actions to prevent it. I believe it is 
inefficient and inhumane. Making a routine  check of submitted data at a bit 
lower level would reduce a temptation to overestimate the unclearly defined 
quality statistics and make the model fabrication more difficult to accomplish. 
Many people do it unknowingly, and catching them afterwards makes no good.

I suggested to turn the current incidence, which might be too complex for 
burning heretics, into something productive that is done as soon as possible, 
something that will prevent fraud from occurring.

Since my persistent trolling at ccp4bb did not take any effect (until now), I 
wrote a bad-English letter to the PDB administration, encouraging them to 
take urgent actions. Those who are willing to count grammar mistakes in it can 
reading the message below.

With best regards,
Alexander Aleshin, staff scientist
Sanford-Burnham Medical Research Institute 
10901 North Torrey Pines Road
La Jolla, California 92037

Dear PDB administrators;

I am wringing to you regarding the recently publicized story about submission 
of calculated structural factors to the PDB entry 3k79 
(http://journals.iucr.org/f/issues/2012/04/00/issconts.html). This presumable 
fraud (or a mistake) occurred just several years after another, more massive 
fabrication of PDB structures (Acta Cryst. (2010). D66, 115) that affected many 
scientists including myself. The repetitiveness of these events indicates that 
the current mechanism of structure validation by PDB is not sufficiently 
robust. Moreover, it is completely incapable of detecting smaller mischief such 
as overestimation of the data resolution and quality.

There are two approaches to handling fraud problems: (1) raising 
policing and punishment, or (2) making a fraud too difficult to implement. 
Obviously, the second approach is more humane and efficient.

This issue has been discussed on several occasions by the ccp4bb 
community, and some members began promoting the idea of submitting raw 
crystallographic images as a fraud repellent. However, this validation approach 
is not easy and cheap, moreover, it requires a considerable manpower to conduct 
it on a day-to-day basis. Indeed, indexing data sets is sometimes a nontrivial 
problem and cannot be accomplished automatically. For this reason, submitting 
the indexed and partially integrated data (such as .x files from HKL2000 or the 
output.mtz file from Mosfilm) appears as a cheaper substitute to the image 
storing/validating.

Analysis of the partially integrated data provides almost same 
means to the fraud prevention as the images.  Indeed, the observed cases of 
data fraud suggest that they would likely be attempted by a 
biochemist-crystallographer, who is insufficiently educated to fabricate the 
partially processed data. A method developer, on contrary, does not have a 
reasonable incentive to forge a particular structure, unless he teams up with a 
similarly minded biologist. But the latter scenario is very improbable and has 
not been detected yet.

The most valuable benefit in using the partially processed data as 
a validation tool would be the standardization of definition for the data 
resolution and detection of inappropriate massaging of experimental data.

Implementation of this approach requires minuscule adaptation of 
the current system, which most of practicing crystallographers would accept (in 
my humble opinion). The requirement to the data storage would be only ~1000 
fold higher than the current one, and transferring the new data to PDB could be 
still done over the Internet. Moreover, storing the raw data is not required 
after the validation is done.

A program such as Scala of CCP4 could be easily adopted to process 
the validation data and compare them with a conventional set of structural 
factors.  Precise consistency of the two sets is not necessary. They only need 
to agree within statistically 

[ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
Can MOSFLM work with image files of type .x (BNL X6A) ? I am having no luck...
I know it can do .cbf (BNL X25) for instance.
Thanks a lot


[ccp4bb] Position in Structural Biology of Signaling

2012-04-05 Thread Qiang Chen
There is an immediate opening for a protein crystallographer position in
Harvard Medical School’s Children’s Hospital. The research is focused on
the structural and functional investigation of Wnt signaling pathway. The
project is the close collaborative efforts between Professors Xi He and
Jia-huai Wang’s labs.

The successful candidate should have a Ph.D. in structural biology. The
candidate will be responsible for determining crystal structure using
X-ray crystallography. He/she should also have experience in molecular
biology and protein biochemistry.

Interested candidates can email a CV, three contacts for reference, as
well as an email address and a telephone number to Dr. Jia-huai Wang at
jw...@red.dfci.harvard.edu or Dr. Xi He at xi...@childrens.harvard.edu.
For more information regarding the Wang and He Laboratories, please see
the website: http://wang.dfci.harvard.edu and
http://www.childrenshospital.org/cfapps/research/data_admin/Site160/mainpageS160P0.html



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


[ccp4bb] postdoctoral position at the NIH focused on understanding the mechanism of cytoskeletal regulators

2012-04-05 Thread ANTONINA ROLL-MECAK
Postdoctoral positions are available in the Cell Biology and  
Biophysics Unit headed by Dr. Antonina Roll-Mecak at the National  
Institute of Neurological Disorders and Stroke. The Roll-Mecak  
Laboratory is interested in understanding the interplay between  
microtubules and their regulators and how tubulin post-translational  
modifications tune the behavior of motors and microtubule associated  
proteins (see for instance Szyk et al., 2011. Nature Struct.  Molec.  
Biol. 8(11): 1250-8; Roll-Mecak, A. and Vale, R.D. 2008. Nature,  
451(7176):363-7; Roll-Mecak, A. and McNally, F.J. 2010. Curr. Opin.  
Cell Biol., 22(1):96-103). We use a combination of biochemistry,  
structural biology, cell biology and single-molecule fluorescence  
techniques. Thus, a postdoctoral fellow in the lab would have the  
opportunity to move between these techniques and build upon an already  
strong background in one of these areas.  We value a vibrant and  
collaborative environment where lab members share ideas, reagents and  
expertise and want to work on fundamental problems in cytoskeletal  
biology.


The Roll-Mecak lab is located in the Porter Center for Neuroscience on  
the NIH main campus in Bethesda. The NIH has a long tradition of  
research excellence in cytoskeletal biology and offers a stimulating  
environment for postdoctoral fellows interested in interdisciplinary  
training in cell biology and biophysics. The research facilities at  
NIH are outstanding and the lab has state-of-the-art equipment such as  
crystallization robots, liquid handling systems, TIRF and confocal  
microscopes. For more information, please visit: http://intra.ninds.nih.gov/rm_lab/


The position will be fully funded by the NIH, and is available  
immediately. We are looking for candidates who wish to work on  
mechanistic problems related to the microtubule cytoskeleton and have  
a strong background in at least two of these areas: molecular biology,  
protein biochemistry, structural biology, cell biology, microscopy or  
single molecule motor biophysics.


Other details: candidates should preferably have less than 2 years of  
postdoctoral experience. Please send a CV, a one-page research  
experience summary, and contact information of three references to anton...@mail.nih.gov 
  Please write “Postdoctoral application” in the subject header.

Re: [ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
thanks for kindly pointing that out. (despite the level of stupidity on my part)
Those were not the raw imgs... They were denzo output files. Its been a while.


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Ronald E Stenkamp
This discussion has been interesting, and it's provided an interesting forum 
for those interested in dealing with fraud in science.  I've not contributed 
anything to this thread, but the message from Alexander Aleshin prodded me to 
say some things that I haven't heard expressed before.

1.  The sky is not falling!  The errors in the birch pollen antigen pointed out 
by Bernhard are interesting, and the reasons behind them might be troubling.  
However, the self-correcting functions of scientific research found the errors, 
and current publication methods permitted an airing of the problem.  It took 
some effort, but the scientific method prevailed.   

2.  Depositing raw data frames will make little difference in identifying and 
correcting structural problems like this one.  Nor will new requirements for 
deposition of this or that detail.  What's needed for finding the problems is 
time and interest on the part of someone who's able to look at a structure 
critically.  Deposition of additional information could be important for that 
critical look, but deposition alone (at least with today's software) will not 
be sufficient to find incorrect structures.

3.  The responsibility for a fraudulent or wrong or poorly-determined structure 
lies with the investigator, not the society of crystallographers.  My political 
leanings are left-of-central, but I still believe in individual responsibility 
for behavior and actions.  If someone messes up a structure, they're 
accountable for the results.  

4.  Adding to the deposition requirements will not make our science more 
efficient.  Perhaps it's different in other countries, but the administrative 
burden for doing research in the United States is growing.  It would be 
interesting to know the balance between the waste that comes from a wrong 
structure and the waste that comes from having each of us deal with additional 
deposition requirements.  

5.  The real danger that arises from cases of wrong or fraudulent science is 
that it erodes the trust we have in each others results.  No one has time or 
resources to check everything, so science is based on trust.  There are efforts 
underway outside crystallographic circles to address this larger threat to all 
science, and we should be participating in those discussions as much as 
possible.  

Ron

On Thu, 5 Apr 2012, aaleshin wrote:

 Dear John,Thank you for a very informative letter about the IUCr activities 
 towards archiving the experimental
 data. I feel that I did not explain myself properly. I do not object 
 archiving the raw data, I just believe
 that current methodology of validating data at PDB is insufficiently robust 
 and requires a modification.
 Implementation of the raw image storage and validation will take a 
 considerable time, while the recent
 incidents of a presumable data frauds demonstrate that the issue is urgent. 
 Moreover, presenting the
 calculated structural factors in place of the experimental data is not the 
 only abuse that the current
 validation procedure encourages to do. There might be more numerous 
 occurances of data massaging like
 overestimation of the resolution or data quality, the system does not allow 
 to verify them. IUCr and PDB
 follows the American taxation policy, where the responsibility for a fraud is 
 placed on people, and the agency
 does not take sufficient actions to prevent it. I believe it is inefficient 
 and inhumane. Making a routine
  check of submitted data at a bit lower level would reduce a temptation to 
 overestimate the unclearly defined
 quality statistics and make the model fabrication more difficult to 
 accomplish. Many people do it unknowingly,
 and catching them afterwards makes no good.
 
 I suggested to turn the current incidence, which might be too complex for 
 burning heretics, into something
 productive that is done as soon as possible, something that will prevent 
 fraud from occurring.
 
 Since my persistent trolling at ccp4bb did not take any effect (until now), 
 I wrote a bad-English letter
 to the PDB administration, encouraging them to take urgent actions. Those who 
 are willing to count grammar
 mistakes in it can reading the message below.
 
 With best regards,
 Alexander Aleshin, staff scientist
 Sanford-Burnham Medical Research Institute 
 10901 North Torrey Pines Road
 La Jolla, California 92037
 
 Dear PDB administrators;
 
 I am wringing to you regarding the recently publicized story about submission 
 of calculated structural factors
 to the PDB entry 3k79 
 (http://journals.iucr.org/f/issues/2012/04/00/issconts.html). This presumable 
 fraud (or
 a mistake) occurred just several years after another, more massive 
 fabrication of PDB structures (Acta Cryst.
 (2010). D66, 115) that affected many scientists including myself. The 
 repetitiveness of these events indicates
 that the current mechanism of structure validation by PDB is not sufficiently 
 robust. Moreover, it is
 completely incapable of 

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bernhard Rupp (Hofkristallrat a.D.)
I also don't really worry about the images as a primary means of fraud
prevention, although such may be
a useful side effect. These cases are spectacular but so rare that it indeed
would not primarily justify the effort. 
That it can be a useful political instrument to make that argument and get
funding, may be, but that is a bit
of a double edged sword and harm can be done see (5)

The real point to me seems - 
a) is there something in the images and in between casually indexed main
reflections we do not use 
right now that allows us to ultimately get better structures?
I think there is, and it has been told before, from superstructures,
modulation, diffuse contributions etc etc.
A processed data file does not help here. But do we need the old image data
for that or rather use new ones from
modern detectors? Where is the cost/benefit cutoff here? 

b) looking at how some structures are refined, there is little reason to
believe that data processing would be done more
competently by untrained casual users (except that much of the data
processing is done with the help of beam
line personnel who rather know how to do it). Had we images, the next step
then could be PDB_reprocess. 
A processed data file does not help much there either.

c) Discarding your primary data is generally considered bad form...
 
@AlexA:  Arguing with the PDB is not really useful. They did not generate
the bad data.

Best, BR

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald
E Stenkamp
Sent: Thursday, April 05, 2012 1:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication

This discussion has been interesting, and it's provided an interesting forum
for those interested in dealing with fraud in science.  I've not contributed
anything to this thread, but the message from Alexander Aleshin prodded me
to say some things that I haven't heard expressed before.

1.  The sky is not falling!  The errors in the birch pollen antigen pointed
out by Bernhard are interesting, and the reasons behind them might be
troubling.  However, the self-correcting functions of scientific research
found the errors, and current publication methods permitted an airing of the
problem.  It took some effort, but the scientific method prevailed.   

2.  Depositing raw data frames will make little difference in identifying
and correcting structural problems like this one.  Nor will new requirements
for deposition of this or that detail.  What's needed for finding the
problems is time and interest on the part of someone who's able to look at a
structure critically.  Deposition of additional information could be
important for that critical look, but deposition alone (at least with
today's software) will not be sufficient to find incorrect structures.

3.  The responsibility for a fraudulent or wrong or poorly-determined
structure lies with the investigator, not the society of crystallographers.
My political leanings are left-of-central, but I still believe in individual
responsibility for behavior and actions.  If someone messes up a structure,
they're accountable for the results.  

4.  Adding to the deposition requirements will not make our science more
efficient.  Perhaps it's different in other countries, but the
administrative burden for doing research in the United States is growing.
It would be interesting to know the balance between the waste that comes
from a wrong structure and the waste that comes from having each of us deal
with additional deposition requirements.  

5.  The real danger that arises from cases of wrong or fraudulent science is
that it erodes the trust we have in each others results.  No one has time or
resources to check everything, so science is based on trust.  There are
efforts underway outside crystallographic circles to address this larger
threat to all science, and we should be participating in those discussions
as much as possible.  

Ron

On Thu, 5 Apr 2012, aaleshin wrote:

 Dear John,Thank you for a very informative letter about the IUCr 
 activities towards archiving the experimental data. I feel that I did 
 not explain myself properly. I do not object archiving the raw data, I
just believe that current methodology of validating data at PDB is
insufficiently robust and requires a modification.
 Implementation of the raw image storage and validation will take a 
 considerable time, while the recent incidents of a presumable data 
 frauds demonstrate that the issue is urgent. Moreover, presenting the 
 calculated structural factors in place of the experimental data is not 
 the only abuse that the current validation procedure encourages to do. 
 There might be more numerous occurances of data massaging like 
 overestimation of the resolution or data quality, the system does not 
 allow to verify them. IUCr and PDB follows the American taxation 
 policy, where the responsibility for a fraud is placed on people, and 
 the agency 

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Well, looks like my opinion about importance of data validation at the moment 
of their submission does not catch much support, it is sad but understandable. 

Automatic redoing the pdb structures by professionals is a good idea, I myself 
suggested a similar thing 10 years ago at Accelrys (we were developing a tool 
that allowed detecting and remodeling changes in protein-ligand structures due 
to ligand binding), but  there was not much financial interest. How much the 
raw images would enhance the remodeling process is an open question, but good 
luck in getting it funded. 

 c) Discarding your primary data is generally considered bad form...
Agreed, but it is a big burden on labs to maintain archives of their raw data 
indefinitely. Even IRS allows to discard them after some time. What is wrong 
with partially integrated data in terms of structure validation? 

 @AlexA:  Arguing with the PDB is not really useful. 
I did not argue yet, but I'll take your advice.

 They did not generate the bad data.
This is a genuine American thinking! But they might create conditions that 
would prevent their deposition.

I think I should stop heating up this discussion. 

Regards,
Alex

On Apr 5, 2012, at 2:11 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:

 I also don't really worry about the images as a primary means of fraud
 prevention, although such may be
 a useful side effect. These cases are spectacular but so rare that it indeed
 would not primarily justify the effort.
 That it can be a useful political instrument to make that argument and get
 funding, may be, but that is a bit
 of a double edged sword and harm can be done see (5)
 
 The real point to me seems -
 a) is there something in the images and in between casually indexed main
 reflections we do not use
 right now that allows us to ultimately get better structures?
 I think there is, and it has been told before, from superstructures,
 modulation, diffuse contributions etc etc.
 A processed data file does not help here. But do we need the old image data
 for that or rather use new ones from
 modern detectors? Where is the cost/benefit cutoff here?
 
 b) looking at how some structures are refined, there is little reason to
 believe that data processing would be done more
 competently by untrained casual users (except that much of the data
 processing is done with the help of beam
 line personnel who rather know how to do it). Had we images, the next step
 then could be PDB_reprocess.
 A processed data file does not help much there either.
 
 c) Discarding your primary data is generally considered bad form...
 
 @AlexA:  Arguing with the PDB is not really useful. They did not generate
 the bad data.
 
 Best, BR
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald
 E Stenkamp
 Sent: Thursday, April 05, 2012 1:04 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
 
 This discussion has been interesting, and it's provided an interesting forum
 for those interested in dealing with fraud in science.  I've not contributed
 anything to this thread, but the message from Alexander Aleshin prodded me
 to say some things that I haven't heard expressed before.
 
 1.  The sky is not falling!  The errors in the birch pollen antigen pointed
 out by Bernhard are interesting, and the reasons behind them might be
 troubling.  However, the self-correcting functions of scientific research
 found the errors, and current publication methods permitted an airing of the
 problem.  It took some effort, but the scientific method prevailed.
 
 2.  Depositing raw data frames will make little difference in identifying
 and correcting structural problems like this one.  Nor will new requirements
 for deposition of this or that detail.  What's needed for finding the
 problems is time and interest on the part of someone who's able to look at a
 structure critically.  Deposition of additional information could be
 important for that critical look, but deposition alone (at least with
 today's software) will not be sufficient to find incorrect structures.
 
 3.  The responsibility for a fraudulent or wrong or poorly-determined
 structure lies with the investigator, not the society of crystallographers.
 My political leanings are left-of-central, but I still believe in individual
 responsibility for behavior and actions.  If someone messes up a structure,
 they're accountable for the results.
 
 4.  Adding to the deposition requirements will not make our science more
 efficient.  Perhaps it's different in other countries, but the
 administrative burden for doing research in the United States is growing.
 It would be interesting to know the balance between the waste that comes
 from a wrong structure and the waste that comes from having each of us deal
 with additional deposition requirements.
 
 5.  The real danger that arises from cases of wrong or fraudulent science is
 that it erodes 

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bernhard Rupp (Hofkristallrat a.D.)
Ojweh

 c) Discarding your primary data is generally considered bad form...
Agreed, but it is a big burden on labs to maintain archives of their raw
data indefinitely. 
Even IRS allows to discard them after some time. 

But you DO have to file in the first place, right? How long to keep is an
entirely different question. 

 What is wrong with partially integrated data in terms of structure
validation? 

Who thinks something is wrong with that idea? Section 3.1 under figure 3 of
said incendiary pamphlet 
states:  '...yadayadawhen unmerged data or images for proper
reprocessing are not available
owing to the unfortunate absence of a formal obligation to deposit unmerged
intensity data or diffraction images.'

 They did not generate the bad data.
This is a genuine American thinking! 

Ok, the US citizens on BB might take this one up on my behalf, gospodin ;-)
видеть вас на Лубянке.

But they might create conditions that would prevent their deposition.

Sure. We are back to the 2007 Reid shoe bomber argument. If you make PDB
deposition
a total pain for everybody, you don't get compliance, you get defiance. Ever
seen
any happy faces in a TSA check line? 

Anyhow, image deposition will come.

Over and out, BR 


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Alright, if the image deposition is the only way out, then I am for it, but 
please make sure that synchrotrons will do it for me...

On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:

 Ojweh
 
 c) Discarding your primary data is generally considered bad form...
 Agreed, but it is a big burden on labs to maintain archives of their raw
 data indefinitely. 
 Even IRS allows to discard them after some time. 
 
 But you DO have to file in the first place, right? How long to keep is an
 entirely different question. 
 
 What is wrong with partially integrated data in terms of structure
 validation? 
 
 Who thinks something is wrong with that idea? Section 3.1 under figure 3 of
 said incendiary pamphlet 
 states:  '...yadayadawhen unmerged data or images for proper
 reprocessing are not available
 owing to the unfortunate absence of a formal obligation to deposit unmerged
 intensity data or diffraction images.'
 
 They did not generate the bad data.
 This is a genuine American thinking! 
 
 Ok, the US citizens on BB might take this one up on my behalf, gospodin ;-)
 видеть вас на Лубянке.
 
 But they might create conditions that would prevent their deposition.
 
 Sure. We are back to the 2007 Reid shoe bomber argument. If you make PDB
 deposition
 a total pain for everybody, you don't get compliance, you get defiance. Ever
 seen
 any happy faces in a TSA check line? 
 
 Anyhow, image deposition will come.
 
 Over and out, BR 
 
 


Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bosch, Juergen
How should they ?
They have no clue which of the 20 datasets was actually useful to solve your 
structure.

If you ask James Holton he has (suggested) to go back to the archived data 
after a certain time and try to solve the undeposited structures then :-)
[Where is James anyhow ? Haven't seen a post recently from him]
Seriously, I think it is in our own interest to submit the corresponding images 
which led to a structure solution somewhere. And as others mentioned bad data 
or good data can always serve for educational purposes.
Just as an example
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/1Y13

Jürgen

On Apr 5, 2012, at 11:46 PM, aaleshin wrote:

 Alright, if the image deposition is the only way out, then I am for it, but 
 please make sure that synchrotrons will do it for me...
 
 On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
 
 Ojweh
 
 c) Discarding your primary data is generally considered bad form...
 Agreed, but it is a big burden on labs to maintain archives of their raw
 data indefinitely. 
 Even IRS allows to discard them after some time. 
 
 But you DO have to file in the first place, right? How long to keep is an
 entirely different question. 
 
 What is wrong with partially integrated data in terms of structure
 validation? 
 
 Who thinks something is wrong with that idea? Section 3.1 under figure 3 of
 said incendiary pamphlet 
 states:  '...yadayadawhen unmerged data or images for proper
 reprocessing are not available
 owing to the unfortunate absence of a formal obligation to deposit unmerged
 intensity data or diffraction images.'
 
 They did not generate the bad data.
 This is a genuine American thinking! 
 
 Ok, the US citizens on BB might take this one up on my behalf, gospodin ;-)
 видеть вас на Лубянке.
 
 But they might create conditions that would prevent their deposition.
 
 Sure. We are back to the 2007 Reid shoe bomber argument. If you make PDB
 deposition
 a total pain for everybody, you don't get compliance, you get defiance. Ever
 seen
 any happy faces in a TSA check line? 
 
 Anyhow, image deposition will come.
 
 Over and out, BR 
 
 

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/






Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Did you play as a child a game called a broken phone? It is when someone 
tells something quickly to a neighbor, and so on until the words come back to 
the author. Very funny game. 

My original thesis was that downloading/depositing the raw images would be a 
pain in the neck for crystallographers, so why would not to begin with the 
partially processed data, like .x files from HKL2000?  People should be trained 
to hardships gradually...



On Apr 5, 2012, at 8:57 PM, Bosch, Juergen wrote:

 How should they ?
 They have no clue which of the 20 datasets was actually useful to solve your 
 structure.
 
 If you ask James Holton he has (suggested) to go back to the archived data 
 after a certain time and try to solve the undeposited structures then :-)
 [Where is James anyhow ? Haven't seen a post recently from him]
 Seriously, I think it is in our own interest to submit the corresponding 
 images which led to a structure solution somewhere. And as others mentioned 
 bad data or good data can always serve for educational purposes.
 Just as an example
 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/1Y13
 
 Jürgen
 
 On Apr 5, 2012, at 11:46 PM, aaleshin wrote:
 
 Alright, if the image deposition is the only way out, then I am for it, but 
 please make sure that synchrotrons will do it for me...
 
 On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
 
 Ojweh
 
 c) Discarding your primary data is generally considered bad form...
 Agreed, but it is a big burden on labs to maintain archives of their raw
 data indefinitely. 
 Even IRS allows to discard them after some time. 
 
 But you DO have to file in the first place, right? How long to keep is an
 entirely different question. 
 
 What is wrong with partially integrated data in terms of structure
 validation? 
 
 Who thinks something is wrong with that idea? Section 3.1 under figure 3 of
 said incendiary pamphlet 
 states:  '...yadayadawhen unmerged data or images for proper
 reprocessing are not available
 owing to the unfortunate absence of a formal obligation to deposit unmerged
 intensity data or diffraction images.'
 
 They did not generate the bad data.
 This is a genuine American thinking! 
 
 Ok, the US citizens on BB might take this one up on my behalf, gospodin ;-)
 видеть вас на Лубянке.
 
 But they might create conditions that would prevent their deposition.
 
 Sure. We are back to the 2007 Reid shoe bomber argument. If you make PDB
 deposition
 a total pain for everybody, you don't get compliance, you get defiance. Ever
 seen
 any happy faces in a TSA check line? 
 
 Anyhow, image deposition will come.
 
 Over and out, BR 
 
 
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://web.mac.com/bosch_lab/