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

[Natesh Ramanathan]

Dear Irina,

If you are not sure of the position of side chain (say Eg. Tryptophan
(Trp)) and there are no EM densities and you want to keep the coordinates
of side chain, you can still keep the coordinates but make the Occupancies
to be zero.  In that way you are basically saying it Trp residue in that
positoin and that these atom positions do not have any electron density.


Cheers,
Natesh

On 2 December 2014 at 13:13, Irina Gutsche <gutsche at embl.fr> wrote:

> 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,
> France
>
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-- 
----------------------------------------------------------
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
----------------------------------------------------------
Dr. Ramanathan Natesh
Ramalingaswami Fellow-DBT, Assistant Professor
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
1st floor, Dept. of Computer Science & Engg. Building,
CET Campus, Engineering College P.O.,
Trivandrum,  695016, Kerala, India

natesh at iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
http://iisertvm.ac.in/~natesh
Ph. 0091- 471-2599403
Fax.0091-471-2597427
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