[3dem] search on EMDataResource

[Cathy Lawson]

Dear Jacopo,

Please try entering your EMDR search query as follows: 

Fab AND resol:[* TO 6]

For the current week there are 117 EMDB entries.


If you are interested instead in all entries containing antibodies or their fragments with resolution 6 or better:

(Antibody or Fab) AND resol:[* TO 6] 

yields 176 entries.


Additional hints about EMDR search query formulations can be found by clicking on the help (?) button and then “view more examples".


Fab stands for antigen binding fragment, so  "Fab fragment” is a bit redundant.
The latter is not routinely used by deposition authors, so will yield a much smaller search result.

I hope this helps and thanks once again for your feedback.


Cathy



Cathy Lawson
Institute for Quantitative Biomedicine
Rutgers University
cathy.lawson at rcsb.org
848 445 5494




> On Aug 26, 2019, at 8:48 AM, Cathy Lawson <cathy.lawson at rcsb.org> wrote:
> 
> Dear Jacopo,
> 
> Thank you for your feedback on EMDR search. I agree that you should be getting more results for this particular query — we’ll look into it and will get back to you shortly.
> 
> Best wishes,
> 
> Cathy Lawson 
> EMDataResource
> RCSB / Rutgers University
> +1 848 445 5494
> 
> 
>> On Aug 26, 2019, at 08:30, Jacopo Marino <jacopo.marino at psi.ch> wrote:
>> 
>> Dear All,
>> 
>> I'm wondering whether there is a more accurate way of searching for all cryo-EM structures obtained in complex with a Fab fragment than just typing "Fab fragment" in the search field on the EMDataResource database.
>> 
>> Doing this way, I count only 17 structures below 6 A, which sounds little to me. Only 15 structures below 6 by searching for "Fab" only.
>> 
>> Sorry if I've missed anything obvious. Any suggestion is very much appreciated.
>> 
>> Thank you and best regards,
>> 
>> Jacopo.
>> 
>> -- 
>> Dr. Jacopo Marino
>> Laboratory of Biomolecular Research
>> Paul Scherrer Institute
>> OFLB/005
>> 5232 Villigen PSI, Switzerland
>> tel: +41 56 310 5484 (or +41 56 310 5777)
>> e-mail: jacopo.marino at psi.ch
>> 
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> 

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