Biological Small Angle Scattering Group
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DAMAVER Manual
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Typical Model Selection & Averaged Model Generation
This is beta distribution of a set of programs to align ab initio low resolution models (e.g. provided by DAMMIN and/or GASBOR) and to build "the most probable" model.
The program package requires the last version of SUPCOMB
This suite contains following programs:
| DAMAVER: | average aligned models and compute probability map |
| DAMFILT: | filter the averaged model at a given cut-off volume |
| DAMSEL: | compare all models, find most probable and outliers (uses SUPCOMB) |
| DAMSUP: | align all models with the most probable one (uses SUPCOMB) |
| DAMSTART: | generates from the averaged model an input file with fixed core for DAMMIN (for those who wants to refine the averaged model) |
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The command "damaver /a" runs the entire procedure in batch mode using ALL *.pdb files in the current directory
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All the programs can be run separately and interactively. To get help, type "programname /h"
Default output files:
damsel.inp: list of *.pdb files (made by DAMSEL)
damsel.log: comparison made by DAMSEL (input for DAMSUP)
damsup.log: superposition made by DAMSUP (input for DAMAVER)
files *r.pdb (superimposed with the most typical model by DAMSUP, except for the discarded
ones)
damaver.pdb: overall volume after averaging (made by DAMAVER)
damstart.pdb: input file with fixed core for DAMMIN refinement
damfilt.pdb (default final model): filtered volume at half of the excluded volume of damaver.pdb
Last edited :
Thursday, 10 August, 2006