Glossary of attributes associated with PCDDB depositions
Word or phrase Description
CDTool files (.gen format)

As an alternative output, data can be downloaded as a CDTool compatible .gen file.

The content of such files are not meant to adhere strictly to the .gen data conventions, but rather these files are produced in order that PCDDB data may be read into the CDTool programme.

Files generated by the PCDDB are marked with the first line : Generic CD0000001000 where the second word is the PCDDBid of the record. The data within the files is arrange in columns, from left to right:

Wavelength, Final Processed Spectrum, HT values (from raw spectrum 1), Final Processed Spectrum, Blank, Blank, Blank.

The final process spectrum is inserted twice in order to prevent CDTool from re-smoothing the data.

Data Bank A facility which is built upon database technology, but which allows users to both "deposit" and "withdraw" information.
HT Voltage / High Tension Voltage This is a measure of the amount of power some photomultiplier tubes require to detect non-absorbed photons. Typically this value rises as the wavelength of the CD experiment decreases because fewer photons are un-absorbed by the sample. The reliability of the reading is adversely affected by high HT Voltage and sections of spectra recorded with an overly high HT value are often unreliable. Opinion is varied as to how high the value of HT can be before the data should be discarded.
Non Validated data The verified data will be publicly accessible and non-amendable and will fulfil the regulatory targets that the data bank aims to serve. For further information, please see Whitmore, L., Janes, R.W. and Wallace, B.A. (2006) Chirality 18:426-429.
PCD files (.pcd format) The PCDDB has its own ASCII file format to present protein circular dichroism data in a standard way. In general, there are three areas of the file:
  1. Header information - containing non-spectral data from the PCDDB record.
  2. Spectral data - arranged columnwise, containing all of the non-raw data information.
  3. Calibration data - arranged columnwise, containing the calibration spectrum, if available.
PCDDBID Identifying code for PCDDB entries. The format of PCDDBID's is 2 letters ('CD' to denote Circular Dichroism) followed by 10 digits and is notionally split into two sections. The first section of two letters and seven numbers is the base of the PCDDBID and this is distinct between samples. The final three numbers signify different records in a group of records, for instance when a set of experiments for a temperature run are deposited, they will share the same base of the PCDDBID and each spectrum will differ only in the final three numbers.
Record Metadata Record-metadata will adopt the accessibility of the record to which it is attached and will be amendable by the depositor of that data and the databank curators. The purpose of record-metadata is to store information that may change over time, despite the verified record itself being non-amendable. Examples of such information would be to indicate if a record has been made scientifically obsolete by a newer record or to add new links to information about the record which may appear in other facilities. For further information, please see Whitmore, L., Janes, R.W. and Wallace, B.A. (2006) Chirality 18:426-429.
Validated data The verified data will be publicly accessible and non-amendable and will fulfil the regulatory targets that the data bank aims to serve. For further information, please see Whitmore, L., Janes, R.W. and Wallace, B.A. (2006) Chirality 18:426-429.

The PCDDB is a development of the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London and the School of Biological and Chemical Sciences, Queen Mary University of London, UK. It is supported by a grant from the BBSRC. Copyright of the design and implementation of this site are retained by the schools and the authors.


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