Strange outputs from MONSA

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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mchammer
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Joined: 2016.11.20 15:41

Strange outputs from MONSA

#1 Post by mchammer » 2016.11.20 16:05

Hi, I'm new to SAXS data analysis and I'm trying to analyze a protein/DNA complex. Generated .dat files via primus and obtained reasonable looking envelops via DAMMIN.

So I have scattering data for both the apo species and the complex. When I input these as data files into the MONSA web interface with two curves (apo/complex) and two phases (protein/DNA), I obtain pdb solutions that look like spheres of balls (attached). I saw another user on this forum had a similar problem, but solved this issue by increasing Dmax/2. I increased my Dmax/2 input from 73 (half of Dmax from gnom) -> 80 -> 200 and obtained the same spherical output. Any ideas of what I could be doing wrong? I've attached a logfile for the run too (to me total scale factor looks wrong).
Attachments
3_14.pdb
(288.99 KiB) Downloaded 171 times
3_14-0.pdb
(94.52 KiB) Downloaded 166 times
3_14.log
(7.08 KiB) Downloaded 172 times

ckerr
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Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: Strange outputs from MONSA

#2 Post by ckerr » 2016.11.23 11:36

MONSA should produce one .pdb file for each phase. If I remember correctly the -0.pdb file is the solvent phase i.e. it will look like a sphere with a void in the middle where your protein goes.

SaxsMax
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Joined: 2007.08.03 19:16

Re: Strange outputs from MONSA

#3 Post by SaxsMax » 2016.11.24 12:36

Seemingly, something is completely wrong with the modelling,
as the program made just two simulated annealing steps
instead of a hundred. Therefore the solution looks like a ball with mixed beads

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