From: Veronika Brazdova (v.brazdova_at_ucl.ac.uk)
Date: Fri Feb 02 2007 - 12:57:25 CST

Dear Axel,

Thanks for the explanation. I have several pdb files with coordinates,
no trajectories. I am trying to build models of different sizes by adding
chunks of protein and some waters together.

I thought I'd simply take the whole protein and do a selection, but
then I was using "water within 2 of something" and it would just select
the atoms that were within 2 A of something, not the whole water molecule
which has at least one atom within 2 A... So now I to write the atoms to
separate (small) pdb files and edit them by hand (adding all atoms for
each molecule) and then I'd like to put them together. (Not by hand,
preferably, because I'd have to renumber all atoms.)

Any thoughts on this procedure would be also greatly appreciated.

Thanks

Veronika