Welcome to the FAQ/Help

DichroMatch

DichroMatch is a facility for matching spectral nearest neighbours. To create a reference set using createRDS you have two options.

Using the PCDDB

Using a set of identifiers from the PCDDB (e.g. CD0000111000) you can create a list of reference spectra. CreateRDS will search the PCDDB for entries matching your supplied codes and return a reference database containing all the entries it could find. Should an entry be incorrect or absent, you will be notified by a red warning message in the download area.

Since the creation of reference sets is so quick, you will not see a loading bar, instead a 'Download Reference Set' button should appear within one second of you clicking 'submit'. Should you have any problems, please feel free to email.

Using your private data

We realise that some people have private collections of data. For this reason CreateRDS allows you to upload data in one of three forms: .gen, .pcd or plaintext (a two column file comprising wavelength and spectral data separated by one or more spaces). Where data is not in units of Delta Epsilon (DE) or Mean Residue Ellipticity (MRE) you are required to add the concentration, pathlength and weight details for your experiment. This allows us to convert your data into DE.

You can add as many files as you like by clicking on the 'Add File' button. This will automatically add a new file selection box to the bottom of the web form. Should you want to remove the entry you can click the red no entry sign to the right of the new row.

When you are happy with the data click 'submit'. Again, a loading bar will not appear as your results should be processed almost instantly (if you add hundreds of files it could take a little longer). For each file that is processed an entry will be created in your reference dataset, which you can download using the 'Download Reference Set' button. You will be provided with a list of files that CreateRDS couldn't process in a red box in the download area - it's presented by the download button.

DichroWeb

CreateRDS also allows users to create customised reference sets for DichroWeb. However, because DichroWeb makes use of structural annotations, users may be required to include information on associated structural data.

For users that create reference sets from the PCDDB, structural information is retrieved from the PCDDB: both the PDB accession code (e.g. 3CHY) and the secondary structure derivations (computed from DSSP using the assignments described in Sreerama, Venyaminov and Woody).

Errors are presented as with the DichroMatch reference sets. There are also two files to download: one contains secondary structure information; the second contains spectral data. Both files are formatted to be compliant with CDPro (as required by DichroWeb).

Users that wish to upload private data collections can do so using the same web form as described above. In addition users are required to include a PDB identifier alongside each of the uploaded files. This is used to retrieve secondary structure definitions from DSSP that are then converted to match the secondary structure scheme as described above.

This feature is in alpha at the moment, currently users cannot upload reference datasets to DichroWeb.

Help

It's not working! Please feel free to send me an email, I would be happy to help you (and for you to help me fix bugs).