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PubMed Entrez BLAST OMIM Taxonomy Structure

Structure Links
NCBI Structure Group
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Linking to Various Servers for the Structure Group
Linking to nrpdbsrv
Linking to mmdbsrv
Linking to vastsrv

Linking to nrpdbsrv

You 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.

Name Possible Values
nrlevel 0, 1, 2, 3
ltable short, long

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:

http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdbsrv.cgi?page=1&pagesize;=20&replist;=Show&nrlevel;=0<able;=short

 

Downloading an ASCII Summary of nrpdb

Use 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:

  • nrlevel: same as above ( 0 ... 3 )
  • pdbcode: the PDB name of the representative chain for the cluster
  • chainid: the specific chain in the sequence for this cluster
WARNING:
  • specifying a chainid for a single-chain sequence will fail
  • failing to specify a chainid for a multi-chain sequence will fail
Examples:

Browse the cluster for the single chain sequence of a myoglobin (1mbd)

http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdbsrv.cgi?group=Show&nrlevel;=0&pdbcode;=1mbd

Browse the cluster for the B-chain sequence of 1cdk:

http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdbsrv.cgi?group=Show&nrlevel;=0&pdbcode;=1cdk&chainid;=b

 

Linking to mmdbsrv

Linking 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:

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1mbd (using pdbcode) http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1629 (using mmdb id)

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:

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1629&form;=6&db;=t&Dopt;=j

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):

Name Description/Values
submit view/save structure ("view")
save view structure (""), view text ("See"), or save text ("Save")
dopt latest Cn3D (j), Cn3D v1.0 (i), Kinemage (k), or Rasmol (r) viewer
Complexity "Cn3D Subset", "Virtual Bond Model", "All Atom Model", "Up to 5 Models", "Up to 10 Models", "All Models"

 

Linking to vastsrv

Linking to the vast neighbor server requires a minimum of two parameters: (1) the uid, and (2) the domain identifier. For example:

http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?uid=9327&chaindom;=93270100

yields a summary page of the neighboring structures for the A chain ("chaindom=93270100") of sea lamprey hemoglobin ("uid=9327"). From here you can select other parameters including specific neighbor alignments, the preferred structure viewer, etc., or alternatively provide these directly with the URL. For example, to view an alignment of the above chain to Phycocyanin using the Cn3D structure viewer, use the additional parameters:

&submit;=view&action;=0&calltype;=a&chn;_complexity=1&atm;_complexity=1&hit;=640602021

The additional parameters are summarized in the following table:

Name Description
submit view/save alignments ("view") or sort/redisplay ("display")
action view structures (0), view text (1), or save text (2)
calltype use a Cn3D (a), Kinemage (m), or Rasmol (p) viewer
chn_complexity view all chains (0) or aligned chains only (1)
atm_complexity view all atoms (0) or alpha carbon atoms only (1)
hit VAST id(s) for the selected alignment(s)

 
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