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

[Petr Leiman]

On 12/02/2014 11:00 AM, Natesh Ramanathan wrote:
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.

In many graphics programs, zero occupancy atoms participate in molecular surface calculations. I am not sure about electrostatic potential calculations, but they might as well be treated as real atoms there as well. And viola, we have a typical over-interpretation case, which we wanted to avoid in the first place, that leads to wrong drugs, people's deaths and multi-billion dollar lawsuits.

Besides, PDB will be very unhappy to have a structure with lots and lots of zero occupancy atoms (we are discussing a case where only a few side chains are visible). Of course, PDB will accept such a structure because they are not police but an archiving service. The header of such a PDB file will be longer than its ATOM records part (each zero occupancy atom will be listed there).

Petr




Cheers,
Natesh

On 2 December 2014 at 13:13, Irina Gutsche <gutsche at embl.fr<mailto: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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--
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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<mailto:natesh at iisertvm.ac.in>
http://www.researcherid.com/rid/C-4488-2008
http://iisertvm.ac.in/~natesh<http://iisertvm.ac.in/%7Enatesh>
Ph. 0091- 471-2599403
Fax.0091-471-2597427



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Petr Leiman
Laboratory of Structural Biology and Biophysics
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EPFL
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