Ab initio modelling for elongated coiled coil proteins

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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Orlad
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Ab initio modelling for elongated coiled coil proteins

#1 Post by Orlad » 2017.04.19 15:55

Hello,

We are working on elongated coiled coil proteins and are trying to modelling them using ab initio methods. Currently using dammin/f and notice that it seems to struggle with the elongated nature of the proteins and tries to fit "bulk" into the envelope. We have so far used the default parameters for both programmes. What dammin/f parameters would be best for elongated particles? Or are there better ways for modelling these types of elongated particles?

Would appreciate any help or knowledge on this!

Thank you!

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AL
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anisometry = PROLATE

#2 Post by AL » 2017.04.21 14:59

You could set --anisometry=PROLATE in DAMMIF and DAMMIN; you can adjust Anisometry penalty weight in the interactive mode.

In DAMMIF you can set Expected shape to 'extended'.

In DAMMIN you can set Initial DAM to 'cylinder' or 'ellipsoid'.

Orlad
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Re: Ab initio modelling for elongated coiled coil proteins

#3 Post by Orlad » 2017.05.03 17:44

Thank you for your reply!

I cannot find the 'set extended shape to extended' in DAMMIF, (I am using the most up to date version)...?

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AL
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dammif --mode=interactive

#4 Post by AL » 2017.05.08 15:53

Make sure you start dammif in 'INTERACTIVE' mode:

Code: Select all

$ dammif --prefix=test --mode=interactive gnom-file.out
Expected/assumed shape? Select one of: (u) unknown, (c) compact, (e)
extended, (f) flat, (r) ring, (h) compact-hollow, (hs) hollow sphere,
(rc) random chain (default: compact) ................................. :

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