[cmview-users] Preview of features for CMView 2.0

[Henning Stehr]

Here is an outlook on some prospective functionalities the next public
release version CMView 2.0 will provide:

How to use CMView 2.0 for homology modelling:
1. Load the target sequence to be modelled (will open an empty contact map)
2. Find a suitable PDB template (e.g. using
http://toolkit.tuebingen.mpg.de/hhpred)
3. Load template using 'Load second contact map...' in 'Compare' menu
4. When asked, choose 'Needleman-Wunsch' alignment or 'Load alignment
from fasta file' for other alignment (e.g. from HHPred)
5. Select all contacts in second contact map ('Select all contact' in
'Select' menu)
6. Copy contacts to first contact map ('Copy selected contacts from
second to first' in 'Compare menu')
7. Optional: Refine contact map using 'Energy function overlay' and
'Toggle contacts'
8. Create protein model using 'Run distance geometry'
Yet to implement: 6,7

How to use CMView 2.0 for consensus based modelling:
1. Load multiple predictions using 'Load from directory' (e.g. server
models for a Casp target)
2. Discretize contacts using 'discretize' function in 'weighted
contacts' group in status bar
3. Choose a suitable cutoff using weight-histogram
4. Apply discretization using 'Apply' button
5. Optional: Refine contact map using 'Energy function overlay' and
'Toggle contacts'
6. Create protein model using 'Run distance geometry'
Yet to implement: 1,5

How to use CMView for ab-initio modelling:
1. Load target sequence
2. Apply secondary structure prediction
3. Select high scoring contacts using 'DeltaRank' functions and
'Energy function overlay'
4. Add contacts using mouse in 'Toggle contacts' mode
5. Inspect geometric environment of contacts using 'SVoxel' functions
6. Reconstruct using 'Run distance geometry'
7. Inspect contacts which could not be reconstructed using 'Compare
mode' and 'Swap models'
8. Iterate 3-7
Yet to implement: 2 and partly 5,7

There is no fixed schedule for realase of the new version but the
development version is constantly being updated and snapshots are
available upon request.