Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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#1 Post by dirac80 » 2011.11.14 18:57

Hi all,

I'm trying to refine a DAMAVER structure, as suggested by a Svergun's review, by using DAMMIN. When I ran DAMMIN with simmetry, I obtained this error:

DAMSYM --W-: Atom# 1 does not have simmetry mate

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#2 Post by Alex » 2012.01.19 13:16


It would be helpful if you provide additional information and files to reproduce your problem.

1. which command/files did you use for refinement?
2. attach your input file
3. which OS and ATSAS distribution are you using.


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Re: DAMMIN_error_starting_guess_PDB

#3 Post by Yann » 2018.08.05 21:32

Hi all,

I have a similar question. I am currently working on a protein that forms an octamer in solution (we have native MS, SEC-MALLS, DLS, analytical SEC, and SAXS to support this). I am no working on getting an ab initio shape.

I ran DAMMIF multiple times to generate about 20 ab initio models in various symmetries (P1, P2, P4, P8, P22, P42). I then wanted to get a final ab initio model via DAMMIN starting from the damstart model. This works for all, except for P8 and P42. When I try to start a DAMMIN run with those symmetries, I get the error message

Atom #x does not have symmetry mate
Assumed symmetry is P1!

I am running the latest ATSAS on a Mac OSX 10.13.6.

Any help or suggestions would be highly appreciated.

Kind regards,


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Re: DAMMIN_error_starting_guess_PDB

#4 Post by 13vide » 2022.11.23 10:25

I am encountering same problem - did you maage to solve it? Would be happy over some suggestions!

Versions I tried using:
atsas 2.8 on old ubuntu
atsas 3.1.3 on new ubuntu

I generated the models with gasbor in P2, then avereged with damaver in P2, and use damstart for dammin.

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