Re: [modeller_usage] Editing pdb file for a multimer

[Modeller Caretaker <modeller-care@ucsf.edu>]

Francesco Pietra wrote:
> I plan to model a homomultimer by modeling separately each chain and
> then combining the results.

Sure, you could do that - or alternatively, Modeller is quite capable of 
building multimer models from multimer templates 
(http://salilab.org/modeller/9v4/manual/node28.html).

> To this concern, are python scripts
> available for (a) inserting the chain label at position 22 (which was
> not inserted the way I did)

By default, Modeller generates single chain models with no chain ID, and 
multichain models with IDs A, B, C etc. But it is simple to change this 
behavior. Either use rename_segments 
(http://salilab.org/modeller/9v4/manual/node177.html) or assign chain 
IDs directly (http://salilab.org/modeller/9v4/manual/node307.html). You 
can do this in several ways:
1. Read in an existing PDB, assign chain IDs, then write it out (as in
   the examples above).
2. Override automodel.user_after_single_model(), and set the chain IDs
   there, immediately before each generated model is written to disk.
3. Override automodel.special_patches(), and set the chain IDs in there.
   This will have a similar effect to (2), except that the rename is
   done before any restraints are generated, so if you are adding
   user-defined restraints, those will need to use your new chain IDs
   to refer to the atoms.

> (b) renumbering the atom serial number,
> TER inclusive?

Modeller always sets the atom serial numbers starting from 1, so there 
is no way to change that. I'm guessing you want to do this in order to 
combine multiple single-chain PDBs into one. But that's straightforward 
- just concatenate the single-chain PDBs, with a TER record in between; 
most programs won't care that the serial numbers or chain IDs are 
duplicated. But if they do, just read that concatenated file back into 
Modeller using complete_pdb(), then write it out again with 
model.write(). This will automatically reassign the atom serial numbers 
and chain IDs for you.

	Ben Webb, Modeller Caretaker
--
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