[3dem] pdb for near-atomic resolution EM maps

Irina Gutsche gutsche at embl.fr
Mon Dec 1 23:43:08 PST 2014

Dear all,

I would like to deposit a near-atomic resolution map (4.3A) and the 
corresponding atomic model to the respective databases. Given recent 
discussions about overinterpretation of the data I am wondering what 
would be the best way to proceed.
Indeed, some bulky side chains are clearly visible and could be placed 
with confidence, in particular in certain regions of the map (according 
to ResMap local resolution ranges from 3.5A to above 6A), but most of 
them not. And even the criteria of "visibility" and "confidence" are 
subjective. The protein complex is of big pharmaceutical interest and I 
suppose that if the complete pdb with all the side chains is deposited, 
it may be downloaded and used for example for drug design, as a kind of 
"absolute truth", which might be dangerous. However, deposit only the 
c-alpha is probably too restrictive. Another option would be to deposit 
only the side chains we are "sure about", but again, it's subjective, 
and anyway we can only be "sure" at the given resoluition. So what would 
be the most honest and unbiased way to share these results with the 
scientific community, in particular with biologists who are not 
necessarily aware of the overinterpretation/overfitting/validation/etc 
issues in our field but who use our results to design their experiments?

Thank you very much for your all ideas and suggestions,

Best regards,

Irina Gutsche
CNRS, Grenoble,

More information about the 3dem mailing list