GASBOR issue with sequence and symmetry

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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lwc
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Posts: 12
Joined: 2012.07.25 07:52
Location: University of Queensland, Australia

GASBOR issue with sequence and symmetry

#1 Post by lwc » 2015.03.16 04:22

GASBOR doesn't seem to apply an input sequence to symmetry mates.

Let's say I'm modelling a protein with one molecule of 150 residues in the asymmetric unit, in P4 symmetry. So total number of residues 4x150=600. When I input the sequence of just the asymmetric unit (150 residues), I get:

Code: Select all

 WARNING:        450  unknown residues were encountered, TYR assumed
So it assigns the correct sequence to the first 150 residues, and then is using tyrosine for all the copies.

To me, the expected behaviour would be to propagate the sequence of the asymmetric unit to all the symmetry mates.

The workaround is just to duplicate the sequence four times in the input but still give 150 residues in the asymmetric unit, which keeps the program happy but isn't noted in the manual. I'm a bit nervous doing that knowing it's already surprised me here, so it might be better to not give a sequence at all.

I feel it's worth reporting in case someone else runs into this. A symmetric solution with different form factors in one of the symmetry mates doesn't make sense in any situation I can think of.

- Lachlan

SaxsMax
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Joined: 2007.08.03 19:16

Re: GASBOR issue with sequence and symmetry

#2 Post by SaxsMax » 2015.03.16 19:56

Thanks for the report, the issue should be fixed in the next Atsas release.
For the moment the workaround as you correctly mention is to duplicate
the sequence n times (where n is the number of symmetry mates)

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