possible idealize app bug – residues being deleted

[pbradley]

I have just notice the the idealize app is shortening my peptides by cutting out residues in the loop regions – i.e. it is shortening my loops but still maintaining a contiguous chain.

I can provide input files etc to reproduce.

Cheers,
James.

[Anonymous]

What do the occupancy fields look like in the PDB for those loops? They’re probably 0 occupancy. The PDB reader is probably throwing the residues out as invalid (since they weren’t in the electron density from which the structure is made).

You could run them through fixbb instead of idealize (use NATRO for the resfile) – if the same issue occurs it means this is occuring at PDB read in time, not within idealize mode.

[pbradley]

thanks for the reply

yep – I think you are right that this was the cause as I have use the occupancy field for other information in my modelling program.

In any case, I have reverted to using Rosetta++ for idealization as I think it gives better results at the moment.

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