Dear Dirk, David,
>> 2009/3/11 Dirk Kostrewa <kostr...@lmb.uni-muenchen.de>:
>>> Dear Paul,
>>>
>>> this is a feature request: I would like to attach notes to the
>>> structure, like "water or sodium", "alternative conformation?",
>>> "peptide flipped", that should be displayed in the next session
>>> like labels as a "three-dimensional" notebook of what I've already
>>> done or want to do.
There is place-text to do this. That has been available since Coot
0.0.
>>> This can be very useful, especially to avoid
>>> perpetual re-fitting/omitting of the same feature again, or simply
>>> to mark checkpoints. It should be possible to put a note both at
>>> an atomic position or at the pointer position (to mark unexplained
>>> density for instance). The notes could be saved with the session
>>> file or as an external file that could be read into a new session.
>>> Could you please think about adding this feature?
>>>
>> David Briggs wrote:
>> Seconded!
>>
>> That is a fantastic idea - so essentially a label associated with a
>> feature & a set of co-ordinates.
This is exactly what annotated view labels are. This has been
available since 0.3.2. Or am I missing your point? (View descriptions
are displayed in the views panel - not in 3D).
You can add view descriptions using
(add-view-description view-number text)
Kevin Cowtan wrote:
> Hmmm... Could probably be done with MMDB's UDD records. Then notes
> would be attached to atoms (maybe residues?). THis has the advantage
> that if you move the module to a different asymmetric unit you retain
> the comments.
>
> It might be nice to save them in the PDB file as remarks, but while I
> think recent MMDB can read remarks, I'm not sure if it can write them?
>
> Also relevant to future PDB spec.
>
If text is attached to residues/atoms then that is quite involved -
how do you transfer annotations from one molecule to the next? (as you
would surely want to do after cycling with Refmac). This is not
unsolvable, just needs to be thought about so that it happens is as
slick a way as possible. (Yes, it would be nice if after Refmacing (or
as you suggest, Phaser, say) annotation remarks were transfered to the
refined molecule).
If text is attached to a position in space there is no issue of
transferring annotations and you can use place-text. Attached is a
simple piece of code to do that where I add a gui wrapper to place-text
so that you can make a 3D annotation, and save and load those annotations.
Regards,
Paul.
