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SPDBV - Import functions

The "Import" utility of SPDBV allows you to connect directly to a spdbv-server, thereby providing direct access to databases and powerfull computing facilities. Before using this service, you have to fill the "Network preferences" correctly. The following SPDBV-servers are curretly available:

 

DeepViewServer Server name or IP-Number Port
Switzerland: www.swissmodel.unibas.ch 27000
Switzerland - backup - in preparation -  

 

net prefs

 

Currently, the spdbv server supports the the following download functions:

  • PDB files (downloaded from RCSB)
  • ExPDB files (downloaded from SwissModel)
  • SwissModel Result files (downloaded from SwissModel Workspace)
  • ExPDB Blast Results (Results of template searches submitted from Swiss-PdbViewer SwissModel Menu which are downloaded from SwissModel Workspace)
  • Motif Search Results (downloaded from Vital-IT)
  • Electron Density Maps (downloaded from EDS[Ref. 8])
  • Compounds (downloaded from PubChem)
  • SwissProt entries (downloaded from ExPASy)
  • Sequences to Model (downloaded from ExPASy or NCBI)
  • PROSITE definitions (downloaded from ExPASy)
  • Note that you can also type a keyword. Several keywords can be combined by boolen AND (+) and NOT (-). E.g.

    +CRAMBIN -NMR

    The server will then return a list of possible PDB entries. You can download entries into the workspace simply by clicking on the IDs (colored in blue). The first column will return an ExPDB file (only one chain) whereas clicking on the second column returns the original PDB file.
import prefs

Note that if you maintain a service that you feel could be of general interest to the community, I am open to discuss the possibility to add direct submission / retrieval from Swiss-PdbViewer interface.