Paul Emsley wrote:
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.
Great- although I have to say "Are you sure?" dialogs are an evil that
should be avoided - they drive me mad! (the Undo is sufficient!)
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.
Fantastic.
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.
Mea culpa - that worked beautifully. However, it didn't work all that
well at the start of my model building, presumably because the sequence
identity between molecules was low (lots of polyalanine)....
Many thanks.
Tony.
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