Information Technology Reference
In-Depth Information
9. Saving Output from Database Searches
9.1 Exporting Graphics Files from Cn3D
Structures displayed in Cn3D can be exported as a Portable Network Graphics (PNG) file
from within Cn3D (the Export PNG command in the
File
menu). The structure file itself,
including all annotations and aligned sequences and structures then present in Cn3D, can
also be saved for later launching in Cn3D.
9.2 Saving Individual MMDB Records
Individual MMDB records can be downloaded to a local computer directly from the
Structure Summary page for that record.
Save File
in the
View
bar downloads the file in a
choice of three formats: ASN.1 (select
Cn3D
); PDB (select
RasMol
); or Mage (select
Mage
).
9.3 Saving VAST Alignments
Alignments of VAST neighbors can be downloaded from the VAST Structure Neighbors
page of any MMDB record. By selecting options in the View Alignment row, the
alignment data can be formatted as HTML, text, or mFASTA, and then saved. By
selecting “save file” from the View 3D Structure row, the full ASN.1 alignment file can
be downloaded, including rotational matrices for producing the VAST alignment from
the original PDB files.
10. FTP
10.1 MMDB
Users can download the NCBI Structure databases from the NCBI FTP site:
ftp://ftp.ncbi.nih.gov/mmdb. A Readme file contains descriptions of the contents and
information about recent updates. Within the mmdb directory are four subdirectories that
contain the following data:
x mmdbdata: the current MMDB database (NOTE: these files can not be read
directly by Cn3D)
x vastdata: the current set of VAST neighbor annotations to MMDB records
x nrtable: the current non-redundant PDB database
x pdbeast: table listing the taxonomic classification of MMDB records
10.2 CDD
CDD data can be downloaded from ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd. A Readme file
contains descriptions of the data archives. Users can download the PSSMs for each CD
