Best tool to model a molecule into a SAXS based bead model

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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dhrubai
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Best tool to model a molecule into a SAXS based bead model

#1 Post by dhrubai » 2015.11.03 15:27

Hi,

I am facing a problem while trying to model a molecule into a SAXS based bead model obtained in an ab-initio way (by DAMMIF). I have a crystallography background and thus used to COOT (to model structures using the electron density map as reference). I am looking for a similar tool here, where I can do a rigid body fit and similar operations based on the low res bead model rather than a electron density map.

Any tips?

Thanks in advance
Arnab

ckerr
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Re: Best tool to model a molecule into a SAXS based bead mod

#2 Post by ckerr » 2015.11.10 10:14

Do SUPALM or SUPCOMB do what you need or are you looking for something slightly different?
http://www.embl-hamburg.de/biosaxs/manuals/supalm.html
http://www.embl-hamburg.de/biosaxs/manuals/supcomb.html

dhrubai
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Re: Best tool to model a molecule into a SAXS based bead mod

#3 Post by dhrubai » 2015.11.10 13:08

Thanx a lot for your reply. But I was looking for something with a GUI, which helps me to fit the (say hi-res) model into the ab initio bead (low res) model and edit it at the same time following the bead model.

If I load the output pdbs into a GUI based molecule viewing cum editing tool (eg COOT, Pymol), while editing I don't get any help in keeping my model aligned to the ab initio bead model (as you get in Coot).

ckerr
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Re: Best tool to model a molecule into a SAXS based bead mod

#4 Post by ckerr » 2015.11.11 10:04

The new ATSAS release contains a plugin for PyMOL (also available from https://github.com/emblsaxs/saspy) which allows running supcomb (and many other ATSAS programs) from within PyMOL. Perhaps this is what you are looking for?

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