Hello Modeller Users,
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. Here's an example: Template: ATOM 1 N SER A 2 -6.487 9.533 21.436 1.00 2.23 1SG 2 ATOM 2 CA SER A 2 -5.822 10.328 20.343 1.00 2.86 1SG 3 ATOM 3 CB SER A 2 -6.345 11.788 20.283 1.00 2.67 1SG 4 and model: ATOM 1 N SER 1 -0.662 11.979 19.810 1.00 65.26 1SG 2 ATOM 2 CA SER 1 0.191 12.970 19.122 1.00 65.26 1SG 3 ATOM 3 CB SER 1 -0.325 14.388 19.420 1.00 65.26 1SG 4 Is there a way to force Modeller to print the chain ID? I convert the resulting PDB to charmm format, and some unpleasantness follows because of the missing chain info.
Thanks for your help! Vadim
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. ... > 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
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Modeller Caretaker -
Vadim Patsalo