Vadim Patsalo wrote:
I am building models in the way described in the basic tutorial. I noticed that the completed model PDB is missing the chain ID column. The template I am modelling from has only one chain, A.
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Is there a way to force Modeller to print the chain ID?
Modeller *does* always print the chain ID, but when building single-chain models, it does not assign a chain ID by default (the chain ID is just a single space, thus you won't see it in the PDB file).
It is straightforward to add a chain ID, however. One way is to use the rename_segments() command, either in automodel.user_after_single_model() (which gets called just before the PDB file is written) or in automodel.special_patches() (which gets called when setting up the model topology). The latter is probably better, although note that if you define other patches, restraints, etc. in your script you will then need to change the residue IDs to include chain IDs (e.g. a restraint between residues 1 and 2 would become a restraint between residues 1:A and 2:A).
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage