How DAMMIF consider water shell?

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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dzabelskii
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How DAMMIF consider water shell?

#1 Post by dzabelskii » 2016.09.09 12:01

I am using DAMMIF program in ATSAS-online package. Last time I compared my dummy beads model with PDB file and found out that despite SAXS curves from both models (I used CRYSOL to obtain SAXS curve from PDB file) have nearly similar parameters (Rg, V, etc) PDB structure looks bit smaller than dummy beads model. I guess that this could happen because DAMMIF somehow consider water shell near objects that make this difference. Anyway it would be great if you explain how DAMMIF consider water shell and why such difference could appear besides water shell guess? Thank you in advance.

franke
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Re: How DAMMIF consider water shell?

#2 Post by franke » 2016.09.20 20:44

dzabelskii wrote:[...] it would be great if you explain how DAMMIF consider water shell [...]
Short answer: not. At least not explicitly.

Alexandros
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Re: How DAMMIF consider water shell?

#3 Post by Alexandros » 2016.09.26 14:45

Alternatively you may use DENFERT (http://www.synchrotron-soleil.fr/Recher ... NG/denfert) that takes into account the hydration shell explicitly..

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