4.2 Web and Local Connections
Before you can use the search & download feature it may be necessary to configure the link between the MembraneEditor and the Protein Data Bank. This can be done by opening 'Connection Settings' , located inside the 'Settings' menu in the menu bar.
The appearing dialog inherits 2 categories:
-'Connection', where you perform your settings with regards to the internet connection and
-'RCSB Links', where you can edit the URLs that are used.
By default, the program uses a direct internet connection. In case your connection uses a proxy, you may have to do some configurations. Choose 'Manual proxy configuration' to enable proxy use.
Use the fields in 'Authentification' in order to enter an username and a password; use the fields in 'Address' to enter an IP address and a port number for http and ftp proxy access.
It may be necessary to fill in some fields depending on your system. You can, however test your settings by pressing 'Test Configuration'. The test may take a few seconds and informs you if both http and ftp access can be established.
Note that the http protocol is used for downloading a pdb file from the PDB. Without access, this feature is not available. Ftp access is required for updating the index file.
Edit RCSB Links
Certain URLs are required in order to link with the Protein Data Bank. Those links are already defined and should work currently. It is possible that the structure of the RCSB site, and therefore
those links may change eventually. In this case, you will have to find out the proper links and replace the old ones, using the textfields located in the 'RCSB Links' tab.
There are 4 different URLs used by this program and two additional links to local tools:
|Download Link||Used to retrieve the specified pdb file when using the download function|
|Entries File||Points on the index file used for the search function. Only required for updating|
|Preview Image||The location of the preview image that is shown when selecting a search result|
|Info Page||Links to a specified info page of a pdb file that may be opened in your system browser|
|Jmol Execution Environment||Link to Jmol on your local file system. This must only be changed if you have a new or a custom version of Jmol on your local system, otherwise, the pre-installed Jmol in the Cm2 folder will be used|
|APL@Voro Execution Environment||If APL@Voro is installed on your system, you can define here the path to the file or - if APL@Voro is globally accessible - just type here "aplvoro". Please see 9.6 Analysis of PDB Membrane Files with APL@Voro for more information|
In all predefined links, except in "Entries File", you'll notice the use of the token #PDBCODE# .
This is a keyword which will be replaced by the specified pdb-id each time the link gets used.
- Written by bjoern
- Category: Cm2help 4. The PDB Integration
- Published: 14 September 2013
- Hits: 2132