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Help: My Experiment

Here, you can find help on how to monitor and analyse your experiment.
Experiment Manager
Abbreviation Description
P / R / F / E / X Prepared / Running / Finished / Error / eXpired
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Tasks Manager
Abbreviation Description
P / Q / R / C / F / E Prepared / Queued / Running / Completed / Finished / Error
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Structures Manager
Abbreviation Description
PDB / SA Protein Structure / Selected Atoms with Labels and Coordinates
IDM / CM Intrinsic Distance Matrix / Contact Matrix
AC / RC / CN Absolute Contacts / Relative Contacts / Contact Numbers
VRML Virtual Reality Markup Language
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Analysis Manager Here are some instructions how to analyse your results:
  1. The original input data is given either as a (normalised) distance matrix (DM, NDM) or similarity matrix (SM, NSM).
  2. In order to cluster, combine and compare the results, the matrices are standardised automatically first. This includes the conversion of similarity matrices (SM) into distance matrices (DM), and a normalisation step if necessary, resulting in an standardised distance matrix (SDM). Missing or incorrect values are estimated and corrected accordingly.
  3. Standardised Distance Matrices (SDM) can be combined in order to give a consensus picture. An averaged matrix and a standardised error matrix (SEM) with standard deviations is calculated.
  4. The clustering method can be changed by selecting "Cluster Results" and then pressing the "Change Settings" button.
Abbreviation Description
(N)SM / (N)DM (Normalised) Similarity Matrix / (Normalised) Distance Matrix
SDM / SDV / SEM Standardised Distance Matrix / Standardised Distance Vector / Standardised Error Matrix
CO / CT Clustering Output / Clustering Tree in PHYLIP Format
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