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Structure Links |
Linking to nrpdbsrvYou can set up a link to:Browsing the entire nrpdb:The basic URL and default components of the query string should be:"http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdbsrv.cgi?page=1&pagesize;=20&replist;=Show" In addition to this, you will need to provide (1) the desired level of non-redundancy, and (2) the amount of detail to be included in the resulting table summary. The following table lists the names to be used for these fields and possible values.
Four levels of non-redundancy are available, based on different sequence similarity cutoffs. For nrlevel = 0, two sequences are considered similar if they have a BLAST p value of 10e-7 or less. For nrlevel = 3, two sequences are considered similar only if they are 100% identical. Other accepted values are: nrlevel = 1 (BLAST p value of 10e-40), and nrlevel = 2 (BLAST p value of 10e-80). If the parameter "ltable = short" is used, the resulting table will only list PDB codes for the chains. With "ltable = long", additional information is provided for each chain (e.g., chain id, resolution, number of residues, etc.). Example: browse all of nrpdb at the most stringent level of sequence-similarity, with the table listing only the pdb codes:
Downloading an ASCII Summary of nrpdbUse ftp from the following url to download a text summary of the entire non-redundant structure database: ftp://ftp.ncbi.nih.gov/mmdb/nrtable/ Browsing Individual Clusters of Sequence-similar Chains:In this case, the basic URL is: "http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdbsrv.cgi?group=Show"Additional parameters you must specify are:
Browse the cluster for the single chain sequence of a myoglobin (1mbd)
Browse the cluster for the B-chain sequence of 1cdk:
Linking to mmdbsrvLinking to the mmdb server requires a minimum of one parameter: uid. This field can specify either the standard pdbcode (e.g., 1mbd) or the 1 to 5-digit mmdb identifier. For example: These queries yield a summary page from which you can invoke other options for viewing or retrieving the actual structure and/or its neighbors or related sequences. Alternatively, you can specify these options directly to call up a viewer or save the structure file: will invoke the latest version of Cn3D for structure viewing. Alternatively you can specify options that allow you to view or save the structure file, specify how many models of the structure to include, the atomic level of detail in the structure, or alternative viewers (Kinemage or Rasmol):
Linking to vastsrvLinking to the vast neighbor server requires a minimum of two parameters: (1) the uid, and (2) the domain identifier. For example:
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