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

Melissa Jurica jurica at biology.ucsc.edu
Thu May 20 09:05:40 PDT 2010

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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Begin forwarded message:

> From: Filip Van Petegem <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>
> 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
> http://crg.ubc.ca/VanPetegem/

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