Most facilities come with their own Download page. This Dowload page describes the general concepts of Downloading individual files, groups of files, or even whole databases.
The MRS software can be used to extract individual entries from the following CMBI data banks (as well as a whole series on non-CMBI data banks): DSSP, HSSP, PDBFINDER2, PDBREPORT, PDB_REDO, BDB.
Feel free to look at the MRS user course for more details.
In principle, there is no need to know our data structure. But if you want to occasionally download one or a few individual files with rsync, it might perhaps help.
Our data banks have three types of directory structures. In the simple type all files simply are located in one directory. But in the more complicated type files are split over subdirectories that have the PDB 4-letter code as name. The most complicated organisation has the middle two characters of the PDB 4-letter code as in-between sub-directory. Examples:
The simple type: DSSP. All DSSP files are available in the directory ′dssp′ which in rsync becomes rsync://rsync.cmbi.umcn.nl/dssp/
The protein structure bioinformatics support ′Lists′ are organized like wi-lists/pdb/%%%/1abc/ which in rsync becomes rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/%%%/1abc/ in which ′pdb′ can also become ′redo′ if you want the information for (fully optimized) PDB_REDO files rather than PDB files, and %%% is the code for the type of computation (see the Lists information).
The most complicated directory structure is used so far by PDB_REDO, BDB, and PDBREPORT only. It consists of pdb_redo/%%/PDBi/ in which %% are the middle two characters of the PDB 4-letter code (like ′ab′ for the file 1abc, but also for 4abx and 1abd, etc) and PDBi is the full PDB 4-letter code.
rsync -avz --delete rsync://rsync.cmbi.umcn.nl/DBNAME/ /path_to_in-house_copy/
where DBNAME can be
Please do these rsync jobs between midnight and 8.00 am Dutch time.
The following commands show how data bank files for entry 1abc can be downloaded to the current directory, assuming the entry exists. Be aware though, that when the entry you try to download does not exist, rsync will raise an error. Substitute ′1abc′ with the entry you want to download.
For PDB entries:
rsync -avz rsync://rsync.cmbi.umcn.nl/dssp/1abc.dssp .
For fully optimized PDB_REDO entries:
rsync -avz rsync://rsync.cmbi.umcn.nl/dssp_redo/1abc.dssp .
Native HSSP format:
rsync -avz rsync://rsync.cmbi.umcn.nl/hssp/1abc.hssp.bz2 .
rsync -avz rsync://rsync.cmbi.umcn.nl/hssp3/1abc.hssp.bz2 .
rsync -avz rsync://rsync.cmbi.umcn.nl/pdbfinder/data/1abc.dat .
rsync -avz rsync://rsync.cmbi.umcn.nl/pdbfinder2/data/1abc.dat .
Plain text file:
rsync -avz rsync://rsync.cmbi.umcn.nl/pdbreport/ab/1abc/pdbout.txt .
HTML page with figures:
rsync -avz rsync://rsync.cmbi.umcn.nl/pdbreport/ab/1abc/index.html .
Fully optimized PDB file:
rsync -avz rsync://rsync.cmbi.umcn.nl/pdb_redo/ab/1abc/1abc_final.pdb .
rsync -avz rsync://rsync.cmbi.umcn.nl/bdb/ab/1abc/1abc.bdb
rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/acc/1abc/1abc.acc.bz2 .
rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/redo/acc/1abc/1abc.acc.bz2 .
rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/cc1/1abc/1abc.acc.bz2 .
rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/redo/cc1/1abc/1abc.acc.bz2 .
PDB number of symmetry contacts:
rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/scenes/ss2/1abc/1abc_sym-contacts.sce .
Rsync is the preferred way of obtaining the CMBI's data bank files. However, if your institute's firewall doesn't allow you to use rsync, feel free to work with FTP. Please don't use too much bandwidth and please don't download everything time-and-time again.
The easiest way is to point your web browser to:
and select the data bank directory (bdb, dssp, dssp_redo, hssp, hssp3, pdb, pdb_redo, pdbfinder, pdbfinder2, pdbreport or wi-lists) you want. Then just browse to the file you need.
Alternatively, you can do the same procedure from the command line (assuming your OS is unix). The following example downloads 1abc.dssp and assumes you have read the rsync examples above (so that you will be able to find other data bank files as well, by analogy). Substitute ′1abc′ with the entry you want to download.
First, log in to the ftp server as ′anonymous′ without a password, then change directory and get the file:
ftp ftp.cmbi.umcn.nl anonymous RETURN cd pub/molbio/data cd dssp get 1abc.dssp bye
Rsync is the preferred way of obtaining the CMBI's data bank files. However, if your institute's firewall doesn't allow you to use rsync, feel free to work with wget. Please don't use too much bandwidth and please don't download everything time-and-time again.
The following example downloads 1abc.dssp and assumes your OS is unix and you have read the rsync and ftp examples above (so that you will be able to find other data bank files as well, by analogy). Substitute ′1abc′ with the entry you want to download.
Individual files can also be downloaded from the websites associated with the BDB, PDB_REDO, PDBREPORT, and YASARA scenes data bank.