Dear CCP4BB-ers,
I should have realised that if you ask CCP4BB for feedback, feedback is what
you will get. In spades :-)
Some feedback to your (public and private) feedback:
- colour-blindness - we have switched from dark EMBL green to light EMBL green
to accomodate all kinds of colour-blindness and after double-checking with
Kevin (who gave it a thumbs-up). I think that this colour is actually nicer
and it is also the same colour that we use on our redesigned front page and in
our banners (see http://pdbe.org).
- tooltips - we have shortened these. Once PDBprints are widely used, we will
probably shorten them even further.
- species icons - the minotaur issue was due to a mistake on my Uppsala page
(now fixed). Our graphic-design department is currently sampling beers and
eating bread rolls in order to get inspiration for a separate icon for yeast.
- how to signal absence of feature or data - if you ask 10 different people
(and esp. CCP4 bulletin-board subscribers!) you will get 10 different answers.
Whatever method is chosen, it is part of the learning process, just as you
have to learn what the three colours of a traffic light mean and what all the
road signs mean. Once you get it, you'll never forget it.
If you want to see the new version of PDBprints in action, visit the PDBe
summary page of your favourite PDB entry (e.g., http://pdbe.org/1cbs) or even
a random entry (http://pdbe.org/random).
To see how PDBprints facilitate at-a-glance assessment of a list of search
results (which entries contain DNA? which entries were done by NMR? which
entries contain a ligand? which entries contain mouse protein? are there any
EM structures for this? etc.), try a database query at PDBe
(http://pdbe.org/advancedsearch), for instance:
http://pdbe.org/advancedsearch?text=lac+repressor
If you want to read more about PDBprints, surf to: http://pdbe.org/pdbprints
Thanks for your feedback!
--Gerard
On Thu, 15 Jul 2010, Gerard DVD Kleywegt wrote:
If you were born before the Dutch lost their first World Cup final, you may
remember the days when "everybody" knew that PDB entry 1tim was the structure
of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was
hen egg-white lysozyme, etc. Unfortunately, life for a structural biologist
is not that simple any longer. Nevertheless, occasionally it would be very
handy to get at-a-glance information about some of the crucial details of a
PDB entry or a list of entries.
When the Protein Data Bank in Europe (PDBe; pdbe.org) launched its redesigned
website recently, we also introduced PDBlogos and PDBprints. PDBlogos are
stylised, intuitive icons that convey important information about a PDB entry
(e.g., the experimental technique, the source organism of the sample, or the
presence of a ligand). PDBprints (short for "PDB fingerprints") are
collections of PDBlogos displayed in a specific order, where each icon
represents a well-defined category of information (and where clicking on any
icon will take you to a webpage with more information about that aspect of
the PDB entry of interest).
PDBprints are used in a number of places already, e.g.:
- at the top of PDBe's plain-English summary page for every PDB entry (e.g.:
http://pdbe.org/random)
- in lists of PDBe database-search results (e.g.:
http://pdbe.org/advancedsearch?text=homeobox)
- at the top of EDS summary pages (e.g.:
http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1fcc)
A number of other (structural) bioinformatics resources are also considering
incorporating PDBprints on their webpages. In fact, they are very easy to
include in *any* webpage as evidenced by this page:
http://xray.bmc.uu.se/gerard/structures_pdbprints.html
For a five-minute illustrated introduction to PDBprints (including
instructions on how to include them in your own webpages) point your browser
to:
http://pdbe.org/pdbprints
We hope that you will find PDBprints useful and we value your feedback.
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
[email protected] ..................... pdbe.org
Secretary: Pauline Haslam [email protected]
