FWIW: If you have an 'old' pdb file, just run it through pdbset with no
keywords (other than 'END'), and the 'element column' will be added for you.
Johan
Paul Emsley wrote:
I think Björn means that previous versions of Coot could read archaic
(version 2.3) pdb files and infer the element from the atom name. Now,
in 0.5 that behaviour has gone. (Yes, the element is used for colo[u]ring).
There was a discussion about this (in an mmdb/CCP4 context) on CCP4-dev
recently.
Swings and roundabouts - or the price of progress, perhaps. Coot now
reads PDB version 3.0/3.1 PDB files - we gain the ability to read
modern/"proper" files from Molprobity and PHENIX but lose the ability to
read archaic files (such as from (older?) versions of SOLVE/RESOLVE (I'm
just guessing from what I have been told).
To answer your question then, there is no way in 0.5 to turn back to the
old behaviour. It might be possible in new versions to enable this, but
currently I am against the idea.
Paul.
Steven Sheriff wrote:
Bjorn:
First I presume you mean element field (or column) rather than card.
Second, at least since COOT 0.3, which is when I started using COOT,
it has used the element field to colo[u]r atoms, so this is not new
behavio[u]r.
Steven
Björn Kauppi wrote:
Why is coot 0.5 relying on the element card at the right end of a pdb
file for proper atom colouring?
>> Can one turn back the 0.4.1 behaviour?
Why is coot 0.5 relying on the element card at the right end of a pdb
file for proper atom colouring? Can one turn back the 0.4.1 behaviour ?
--Björn
