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Dear all
I am resending the following email that I sent out at the end of July regarding the Fourier Shell Correlation validation server. We are still very keen on getting feedback and hope that at least some of you will use it to deposit FSC curves to EMDB!
At the 7th February 2013 CCP-EM community meeting I presented PDBe plans to launch EM validation web services to promote and encourage good practices and consistency in reporting results - we currently have fewer than 15 FSC curves in EMDB! As a first step in this process we are rolling out a FSC server for beta testing: http://wwwdev.ebi.ac.uk/pdbe/emdb/fsc/fsc/
You will need to upload two maps and specify the voxel size – it will then calculate the FSC curve and present this result as a plot. It will also calculate and show the 0.5 and 0.143 cut-off resolutions (calculated by linear interpolation from the FSC curve), and it will generate an XML file that can be uploaded as part of your EMDB deposition.
Note: This server does not require any login and is not a part of EMDB deposition so you can use on any data irrespective of whether you plan to submit it to EMDB or not.
In order to go from beta to a production version we need your help in testing the resource!
We are interested in feedback on both technical and scientific aspects of the resource, e.g.:
a) sanity check – does this server produce the same results that you get from other software?
b) what additional information should we collect from the user? (protocol – gold standard, odd/even etc; symmetry; masking)
c) should we display the 3 sigma and half-bit curves and calculate the respective cut-offs?
d) file format issues
e) file size issues
f) features that you would like implemented and any bugs you encounter
We would also like to offer a few more test sets for the FSC server. We are thankful for any pairs of maps you are willing to give us to make publicly available as test data for FSC server.
Please feel free to contact me with feedback and questions: [log in to unmask]
Many thanks and best wishes
Ardan Patwardhan
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Tel: +44 1223 492649