[3dem] pdb for near-atomic resolution EM maps
rkhayat at ccny.cuny.edu
rkhayat at ccny.cuny.edu
Tue Dec 2 08:54:07 PST 2014
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
>
> EPFL
> BSP-415
> CH-1015 Lausanne
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