Feedback and suggestions
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[edit] More stuff!
Why can't this site have more stuff? --Dan 02:38, 27 August 2007 (KST)
- For example, can we categorize structures by publication? It would be nice to be able to browse structures by publication type, journal, author and paper. --Dan 02:48, 27 August 2007 (KST)
- OK, and how about implementing family classification? No good simple 'protein name' ontology exists that I know of... Something like KOG, but for whole proteins. --Dan 02:48, 27 August 2007 (KST)
- Can we implement 'error templates' - a series of templates that mark structures with specific 'errors', such as being Ca only or having other problems. This would be the first steps towards developing standardized datasets for protein structure analysis. --Dan 02:57, 27 August 2007 (KST)
Hi Dan, Can you add a visualizer that opens within Mediawiki? - Jong
- Hey Jong... I think we already did... Can you see http://wiki.jmol.org:81/index.php/MediaWiki ? - Dan.
[edit] Curation of Biological Units
I was wondering if a link to PiQSi could be added for each structure to get info on the biological units: e.g: http://www.supfam.org/elevy/piqsi/piqsi_get.cgi?code=1msd
- Done --Henning 03:28, 30 January 2008 (KST)
PDBwiki is a cool idea! I don't remember seeing a post on the PDB mailing list - maybe it could be advertised?
- There are still some issues to be fixed but we plan to announce it soon --Henning 03:28, 30 January 2008 (KST)
- Update: Has been announced on 2008/04/08.
[edit] Server slow ?
I don't know if it's only now or if it's my connection but the response time of the server seems quite slow.
- One possible reason for this can be that the server is in Korea and overseas traffic is slow --Henning 03:28, 30 January 2008 (KST)
[edit] Remove duplicate chains?
I noticed that new entries have duplicate chains grouped together into one 'entity'. Can you 'update' all the old entries to the new format? What / where is the 'development timetable' ? --Dan 18:13, 6 September 2008 (KST)
- We will do this kind of clean up shortly, when we move to a new server --Henning 01:22, 4 February 2009 (KST)
[edit] Structurally similar proteins?
How can I use PDBWiki to find proteins that are structurally similar to a given PDB ID? --134.36.64.135 16:50, 26 September 2008 (KST)
- Use the link 'Structural Neighbours (Dali Database)' in the 'Analysis Tools' section on the respective structure page, e.g. 1sha --Henning 01:22, 4 February 2009 (KST)
[edit] Default representation model of a protein 3D structure
I wonder who had decided and why to use a CPK model for default representation of a protein structure? With all respect, such a model does not bring much of information when it is not in interactive mode. I would suggest to re-generate all structures in the cartoon (ribbon) view, colored for example in the rainbow color scheme, in order to see both secondary structure elements and identify N- and C-terminals.
If you want, I can help with a PyMol script for batch-mode image generation. Alexey Porollo (POLYVIEW-3D and other proteomics servers)
- Thanks for your suggestion. In fact, we will release an updated version shortly which among many other improvements will also have cartoon visualization. The spacefill representation was chosen to highlight the architecture of larger structures such as virus capsids where this depiction looks less confusing than a cartoon diagram. In any case, you can use your favourite visualization tool with the 'Visualization' links at the bottom of each page. And if your favourite tool is missing, go ahead and add it. It's a Wiki after all!
--Henning 20:44, 22 March 2009 (KST)
