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Access to individual files via MRS

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.

Our data structure

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.

Mirroring entire data banks

rsync -avz --delete rsync://rsync.cmbi.umcn.nl/DBNAME/ /path_to_in-house_copy/

where DBNAME can be

• dssp
• dssp_redo
• hssp
• hssp3
• pdbfinder/data or PDBFIND.TXT for a single file containing all entries
• pdbfinder2/data or PDBFIND2.TXT for a single file containing all entries
• pdbreport
• pdb_redo
• bdb (append ??/????/????.bdb to only download BDB files, skipping other meta files)
• wi-lists/pdb (append /acc, /cc1, /cc2, etc. for specific lists)
• wi-lists/redo (append /acc, /cc1, /cc2, etc. for specific lists)
• wi-lists/pdb/scenes (append /ss2 or /iod for symmetry contacts or ion-site scenes)
• wi-lists/redo/scenes (append /ss2 or /iod for symmetry contacts or ion-site scenes)

Please...

Please do these rsync jobs between midnight and 8.00 am Dutch time.

Access to individual files via rsync.

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.

DSSP

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 .

HSSP

Native HSSP format:

rsync -avz rsync://rsync.cmbi.umcn.nl/hssp/1abc.hssp.bz2 .

Stockholm format:

rsync -avz rsync://rsync.cmbi.umcn.nl/hssp3/1abc.hssp.bz2 .

PDBFINDER

rsync -avz rsync://rsync.cmbi.umcn.nl/pdbfinder/data/1abc.dat .

PDBFINDER2

rsync -avz rsync://rsync.cmbi.umcn.nl/pdbfinder2/data/1abc.dat .

PDBREPORT

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 .

PDB_REDO

Fully optimized PDB file:

rsync -avz rsync://rsync.cmbi.umcn.nl/pdb_redo/ab/1abc/1abc_final.pdb .

etc.

BDB

rsync -avz rsync://rsync.cmbi.umcn.nl/bdb/ab/1abc/1abc.bdb

LISTS

PDB acc:

rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/acc/1abc/1abc.acc.bz2 .

REDO acc:

rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/redo/acc/1abc/1abc.acc.bz2 .

PDB cc1:

rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/cc1/1abc/1abc.acc.bz2 .

REDO cc1:

rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/redo/cc1/1abc/1abc.acc.bz2 .

etc.

YASARA SCENES:

PDB number of symmetry contacts:

rsync -avz rsync://rsync.cmbi.umcn.nl/wi-lists/pdb/scenes/ss2/1abc/1abc_sym-contacts.sce .

etc.

Access to individual files via ftp

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.

Web browser

The easiest way is to point your web browser to:

ftp://ftp.cmbi.umcn.nl//pub/molbio/data/

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.

Command line

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

Access to individual files via wget

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.

wget ftp://ftp.cmbi.umcn.nl/pub/molbio/data/dssp/1abc.dssp

Website access to individual files

Individual files can also be downloaded from the websites associated with the BDB, PDB_REDO, PDBREPORT, and YASARA scenes data bank.