On 30/10/13 12:32, Tim Gruene wrote:
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Dear Andreas,
I am not sure there is a convention, but there has been a decision.
When you deposit a structure with the PDB, they place all ligands
including water molecules to the respective nearest macromolecular
chain. I found this rather annoying the other day as I looked at the
polymerase structure and wanted to take a look at the Zn-atoms.
Instead of navigating through chain Z, where probably many
crystallographers would have put them, I had to check the PDB (text)
file for the correct chain and residue number and enter this into the
'goto'-field of coot.
If I understand some people correctly, this is not a shortcoming of
the PDB-format, but of the software developer developing the software
I used. So I am waiting for the next version of coot/mmdb with voice
recognition where I can just say "Coot, please centre on the next Zn
in this structure". Or at least opening a pop-up window saying "This
is you coot speaking. This structure contains 6 Zn atoms, and I feel
that you are interested in looking at their environment. Please click
'yes' to centre on the next Zn-atom I think is most suitable for you
to look at" ;-)
How about Ctrl-L (het-group navigation)?
Paul.
