Important Notice: Announcing MolIDE1.7 (May 1, 2010):
Some changes in xml2pdb, blastpgp, and formatdb to deal with changes in the PDB and in Uniref and NCBI files.
On some Windows systems, there may be a problem with formatting large databases like nr and uniref100.
The program formatdb.exe splits large databases into multiple files, e.g. nr.00, nr.01, nr.02, etc.
The program creates a file with the extension .pal, such as nr.pal, that lists the individual files, nr.00, nr.01, etc.
On some systems, the .pal includes full pathnames for the list of files, e.g. C:\FCCC\MolIDE\db\nr\nr.00.pin. This causes an error on Windows when running blast. To fix this problem, remove the pathname and leave only the filenames, nr.00.pin, etc.
Important Notice: Announcing MolIDE1.6 (July 1, 2008):
Easy installer for Windows version (highly recommended over Linux installation)
One-step updating of PDB and Non-redundant protein sequence databases (both Linux and Windows)
PSI-BLAST search of non-redundant database can be opened as a sortable table for browsing homologues of query.
List of templates from PDB includes protein names and species.
Works with current remediated XML files from the PDB (unannounced and undocumented changes to PDB files have caused problems in MolIDE in the last year)
NCBI's non-redundant protein database (nr) can be replaced with Uniprot's Uniref100 database:
Under Tools->Servers, change "NR ftp Server" to ftp.uniprot.org
Under Tools->Servers, change "NR ftp server Path (.gz file)" to /pub/databases/uniprot/current_release/uniref/uniref100/uniref100.fasta.gz"
Under Tools->Psiblast, change "NR Seq DB File and Path" to C:\FCCC\MolIDE\db\nr\uniref100 or wherever the uniref100 database is located
MolIDE automatically downloads these large sequence databases (nr or uniref100) and formats them for use with BLAST.
MolIDE has also the capability of stereo3d representation (with anaglyph or shutter glasses) if used in conjunction with a regular (non quad buffered) Nvidia® video card on Microsoft Windows®. Use red/blue anaglyph glasses to view the pictures below. You can get a free pair of glasses here.