DichroWeb FAQ

1.0 General
2.0 Using DichroWeb - submitting data
3.0 Using DichroWeb - generating and understanding the results
4.0 Server Information

1.0 General

Q 1.01	What does DichroWeb do?
A 1.01	DichroWeb is a web interface to several open source algorithms which perform analyses of circular dichroism data.
Q 1.02	Who can use DichroWeb?
A 1.02	DichroWeb is freely available to all academic and non-profit institutions.
Q 1.03	How do I register for DichroWeb?
A 1.03	Our preferred sign up method is for you to complete our on-line application form. After this is filled in, we will send you an agreement to sign and fax (or post) back to us. When we have received the signed agreement we will provide you with an account.
Q 1.04	Why do I need to register for DichroWeb?
A 1.04	The registration process is required because DichroWeb runs on departmental servers and access to these severs has to be regulated.
Q 1.05	Why do I need two different user names and passwords?
A 1.05	This is a security measure for the host servers. The main user name and password gets you into the server and the "UserID" and "IDpassword" identify you individually.
Q 1.06	Can I get DichroWeb on a CD, or installed on my network?
A 1.06	No, DichroWeb is intended to be a web based service, because it removes the hassle of installing and updating software on individual systems.
Q 1.07	Can I see documentation for the analysis algorithms?
A 1.07	Please see the references section and consult the original papers therein.

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2.0 Using DichroWeb - submitting data

Q 2.01	Where do I submit my data?
A 2.01	From the DichroWeb home page, click either the "input data" link on the left hand side or the "Start Analysis" link in the main panel. This will take you to the data submission page where you can complete the form and submit your data file.
Q 2.02	I can't upload my file, what's wrong?
A 2.02	The two main causes of data files not being uploaded correctly are firstly the file location (make sure it is typed or selected correctly) and secondly some web browsers will insert the file name inside quotes when you select a file using the "browse" button. In the second case, remove the quotes before submitting your data.
Q 2.03	My uploaded binary file causes problems, why is this?
A 2.03	Binary files such as .jws files are not accepted by DichroWeb, only files in plain text. Binary files can usually be converted into plain text by the software supplied by the spectrometer manufacturer.
Q 2.04	Which analysis method should I use?
A 2.04	Each of the analysis methods uses a different technique to analyse the data. It is desirable to understand the underlying principles behind the methods and we give the references required for each analysis method. Some data sets will preclude the use of certain methods, but in such cases DichroWeb will refuse to employ a method where the data set is incompatible.
Q 2.05	Which reference data set should I use?
A 2.05	Each reference dataset is made from a collection of proteins of known structure. The best result will in theory come from the reference dataset which is most like the sample, in terms of structure. If the sample is totally unknown in terms of structure, each viable reference dataset should be used and the results examined for their NRMSD value. It should be noted that not all reference datasets may be used for all samples; this is dependant upon the range of data points in the sample and DichroWeb will automatically disallow any incompatible combinations.
Q 2.06	Sometimes I am asked for additional data about sample concentrations and cell path lengths, why is this?
A 2.06	Depending on the input units used and whether you require the results to be displayed in different units from the input, you may be asked for the details about sample concentration, cell path length and the mean residue weight of the sample. DichroWeb uses this information to perform the necessary conversions.
Q 2.07	How does DichroWeb define "Mean Residue Weight" (MRW) ?
A 2.07	This is the mean average value of the individual amino acids in the protein sequence. The value is given by dividing the molecular mass of the peptide by the number of residues in the sequence.
Q 2.08	What happens to the multiple spectra which are recorded in the AVIV 2.86 file format?
A 2.08	At present, only the first spectra in the file will be read and uploaded. The preferred file format from AVIV is the 60-62D type file format.

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3.0 Using DichroWeb - obtaining and understanding results

Q 3.01	I get an error every time I try to submit data - what's happening?
A 3.01	This usually means that part of the information in the input file is wrong or does not match exactly to the information that was uploaded in the data file. In the first instance, check that the input form was completed correctly.
Q 3.02	Sometimes I get a results page, but the pop-up results/graph pages have errors - why is that?
A 3.02	This happens when the analysis produces a null answer. If you experience this, please submit a bug report and include a sample of the data to which it occurs.
Q 3.03	Sometimes I only ever get an 'error report' - why is that?
A 3.03	Usually, persistent errors are due to incorrect input values or poor quality data. Check carefully that the information in the web-form matches up exactly to the data in the input and that everything is in the correct units. If all else fails, please submit a bug report and include a sample of the data which you were using.
Q 3.04	What do "helix 1" "helix 2" "sheet 1" and "sheet 2" mean in the results tables?
A 3.04	We highly recommend that you refer to the publications which accompany each analysis algorithm for a full explanation of their results. See the references section for further information. In particular though, we refer you to this reference : Sreerema, N., Venyaminov, S.Y., and Woody, R.W. (1999) Estimation of the number of helical and strand segments in proteins using CD spectroscopy. Protein Sci. 8, 370-380.
Q 3.05	What are the common potential sources of experimental error that could affect my analysis?
A 3.05	Several things can lead to a poor spectrum during the data collection, they include : Recording a spectrum using the wrong scale or magnitude for the signal, collecting a spectrum which is too noisy (this is especially crucial at low wavelengths), collecting a spectrum where the zero value on the spectrometer has not been set correctly.

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4.0 Server Information

Q 4.01	Did DichroWeb upgrade its hardware recently?
A 4.01	In February 2006, three of the algorithms were recompiled for our new 4 processor server. Selcon3, continLL and CDSSTR should now run somewhere between 2 and 10 times faster, depending on the complexity of the calculations.
Q 4.02	Did the recompilation cause changes in any of the software?
A 4.02	Selcon3 and continLL are unaffected. CDSSTR had to be slightly modified to compile due to some no-longer-supported functions in the code. This is a situation acknowledged by the authors of the algorithm. Our tests show that this has little impact on the majority of calculations, although differences for poor spectra can be (at most) +-3% per structural assignment. If you require more details about this please email the DichroWeb administrator (currently L.Whitmore, add @bbk.ac.uk for the email address).

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