[3dem] Fwd: [ccp4bb] electron microscopy: where open access fails

Edward Egelman egelman at virginia.edu
Thu May 20 09:13:18 PDT 2010

  I have long argued for the public release of published 
reconstructions, and have found it unfortunate that some people have 
published structures and then refused to make them available. This would 
never be tolerated in other fields (imagine sequencing a gene, writing a 
paper about it, and refusing to make the full sequence available). 
Journals can act on this. As Editor-in-Chief of Biophysical Journal I 
would retract a paper after authors refused to make a published 
reconstruction available, since one of the conditions of publication is 
the public availability of those data.
Ed Egelman

Melissa Jurica wrote:
> An issue worth discussion from the ccp4 bulletin board:
> *Melissa Jurica
> *
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Melissa S. Jurica, Ph.D.
> Molecular, Cell & Developmental Biology
> Center for Molecular Biology of RNA
> UC Santa Cruz
> 1156 High Street
> Santa Cruz, CA 95064
> Office: 251 Sinsheimer Labs
> Lab: 237 Sinsheimer Labs 
> Office phone (831) 459-4427
> Lab phone (831) 459-2463
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> http://www.mcd.ucsc.edu/faculty/jurica.html
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> *
> *
> Begin forwarded message:
>> *From: *Filip Van Petegem <filip.vanpetegem at GMAIL.COM 
>> <mailto:filip.vanpetegem at GMAIL.COM>>
>> *Date: *May 18, 2010 4:47:58 PM PDT
>> *Subject: **[ccp4bb] electron microscopy: where open access fails*
>> *Reply-To: *Filip Van Petegem <filip.vanpetegem at GMAIL.COM 
>> <mailto:filip.vanpetegem at GMAIL.COM>>
>> Dear colleagues,
>> whereas data sharing for most crystallographers appears to be a 
>> no-brainer, making coordinates and (most of the time, hopefully) 
>> structure factors available, it seems the electron microscopists are 
>> drastically lagging behind when it comes to making data available.
>> Many cryoEM structures are still being published without the 
>> corresponding maps being deposited in the EM database.  In one 
>> particular case, I was interested in looking at a cryoEM map from a 
>> paper published in a well-renowned open access journal starting.  The 
>> paper contains the EMDB accession codes for the maps, but these maps 
>> appear to be 'on hold' since over a year.  Enquiry with the authors 
>> delivered a firm 'no' in releasing the maps:  they claim it is OK to 
>> keep the maps on hold for 2 years, simply because the EMDB gives the 
>> option to do so.  A further enquiry with the journal editors led to 
>> no avail: despite the clear journal policy on sharing both 
>> manuscripts and data, they were also unable to force the authors to 
>> release their maps, now ~13 months after publication of the paper.  
>> The fact that this was in an open access journal makes this all the 
>> more shocking.
>> It is striking to see how much still has to be done to lift the 
>> cryoEM world up to the same standards as the crystallographic 
>> community (when it comes to sharing data, at least). Structures can 
>> simply be published without anybody being able to check the validity, 
>> let alone use it for obvious experiments such as docking crystal 
>> structures, integrative protein structure modeling, etc.
>> With many structural targets going towards bigger and more 
>> challenging, combining cryoEM data with crystal structures is going 
>> to become more and more important. What can we, crystallographers, do 
>> to stimulate data-sharing in the cryoEM world?
>> (My apologies to the cryoEM people on this bulletin board:  if you 
>> have been making your maps available, you'll agree that clearly not 
>> everybody does...)
>> Filip Van Petegem
>> -- 
>> Filip Van Petegem, PhD
>> Assistant Professor
>> The University of British Columbia
>> Dept. of Biochemistry and Molecular Biology
>> 2350 Health Sciences Mall - Rm 2.356
>> Vancouver, V6T 1Z3
>> phone: +1 604 827 4267
>> email: filip.vanpetegem at gmail.com <mailto:filip.vanpetegem at gmail.com>
>> http://crg.ubc.ca/VanPetegem/
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Edward H. Egelman, Ph.D.


Dept. of Biochemistry and Molecular Genetics
University of Virginia


Biophysical Journal

phone: 434-924-8210
fax: 434-924-5069
egelman at virginia.edu <mailto:egelman at virginia.edu>

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