Dear Oliver,
Antony Oliver wrote:
> Dear Paul + friends,
>
> Would it be possible to place in the (top right?) corner of the main screen (or elsewhere)
> an indicator telling the user what type of restraints are currently being used for real-
> space refinement/fitting? I frequently forget that I have put alpha helix restraints on
> when building, and wonder why my amino acids are drifting so dramatically out of my
> electron density!
We were talking about this problem just recently (at the CCP4 dev
meeting, I think). Yes an iconic indicator would be nice. What would
be more clever, we think (or at least I think we think) is for Coot to
realise that helical (or strand) restraints are active and examine the
"helicalness" ("strandiness") of the fragment that you are trying to
refine - and if it passes a threshold of sufficient difference from
ideality then you get a warning - something along the lines of an "Are
you sure?" dialog.
>
> I think it would also be useful if something similar could also be displayed to indicate
> which map you are using for fitting and refinement - I often have 2fo-fc maps, fo-fc
> maps, and ncs-averaged maps loaded - and often have to switch between them when
> building - and frequently forget which one I am currently using.
Yes, OK. For 0.7.
>
> And, speaking of NCS.... I would really appreciate a script that could superimpose a
> selected molecule onto all the ncs-related molecules and write them all out to a PDB. I
> currently do it manually, by SSM Superpose, change chain ID, and writing out to PDB.
> Which is fine when you only have two or three molecules in the asymmetric unit, but
> when you have more...
The copy-chain function is supposed to do something very like that. If
by "selected molecule" you mean Coot's NCS master chain, then copy-chain
is what you want (Extensions -> NCS -> Copy NCS chain...). If the
"selected molecule" is not part of NCS molecule, you will have to do a
bit of massaging.
Paul.
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