Chain attribute

[Theresa]

Hi all,

(Hopefully) easy question here. I would like to modify the chain of a selection before writing it to a pdb file, but I can't seem to find how to adjust the chain name. I'm using v16, if it matters.

My procedure:

u = mda.Universe(mypdb.pdb)
myatoms = u.select_atoms('segid SEG')

myatoms.chains = 'A'

myatoms.writepdb('newpdb.pdb')


However, there doesn't appear to be a chain or chains attribute. I know MDAnalysis has this information, as when I write the PDB file, there is a chain listed. How do I access this information to change it?

Thank you very much,
Theresa

[Richard Gowers]

Hi Theresa

MDAnalysis treats the chains in a PDB file as segments, so the chains will be referred to as segments.

If you just want to rename the chain, you could do:

myatoms = u.select_atoms('segid SEG')

myatoms.segments.segids = 'NEW'

myatoms.write('new.pdb')

If you want to split a chain into two, there's an extra step of creating a new Segment within the Universe:

myatoms = u.select_atoms('segid SEG')

newseg = u.add_Segment(segid='NEW')

myatoms.segments = newseg

myatoms.write('new.pdb')

Hope that helps, let us know otherwise!

Richard

[Richard Gowers]

Oops, just realised there's a small mistake there, to assign to the new segment it's:

myatoms.residues.segments = newseg

[Theresa]

Hi  Richard,

Thank you very much! That helps.

Theresa