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

[rkhayat at ccny.cuny.edu]

While I agree with everything Petr has said, I must 
disagree with his second to last comment. I have been 
policed by the PDB over trivial matter.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY  10031
Tel. (212) 650-6070
www.khayatlab.org


---- Original message ----
>Date: Tue, 2 Dec 2014 10:25:53 +0000
>From: 3dem-bounces at ncmir.ucsd.edu (on behalf of Petr 
Leiman <petr.leiman at epfl.ch>)
>Subject: Re: [3dem] pdb for near-atomic resolution EM maps  
>To: Natesh Ramanathan <natesh at iisertvm.ac.in>,Irina 
Gutsche <gutsche at embl.fr>
>Cc: "3dem at ucsd.edu" <3dem at ucsd.edu>
>
>   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> 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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> --
> Petr Leiman
> Laboratory of Structural Biology and Biophysics
> http://lbbs.epfl.ch
>
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