Re: [COOT] Add OXT broken?

[Edwin Pozharski]

Funny, but your email consistently crashes my Evolution Email
client.  Not a coot problem, I presume :)

Cheers,

Ed.

 When I try to add an OXT to my model, coot crashes.
Specifically, when I
 try to change the chain from the list in
the popup window (below), it
 hangs then completely crashes.  I'm
on an intel mac running 10.6.8, with
 Coot 0.7-pre-1 (revision
3628).  Bug?
 
 Thanks,
 Jon
 
 


-- 
Edwin Pozharski, PhD
University of
Maryland, Baltimore

[COOT] refine/improve Rama

[Ed Pozharski]

Is there some way to do the Refine/Improve Ramachandran plot not on the
whole molecule?  The underlying command stepped-refine-protein-for-rama
doesn't seem to have any other options but the imol, so obviously no
luck.

I also tried set-refine-ramachandran-angles 1 which, afaiu, should
turn Ramachandran restraints on, but I don't see any difference (in
fact, when I refine a zone the residues move away from allowed angles).
I thought that this could be combined with stepped-refine-protein, but
that one would also tackle the whole thing, and one cannot narrow its
action to a zone.

I could, of course, delete the elements I don't want refined and later
reinsert them.  Another workaround (maybe) is to fix the atoms I don't
want to move (in which case it'd be totally awesome if one could fix all
the atoms in a zone at once - is this possible?).

So, perhaps a future version may allow for all of these operations (e.g 
fit-protein, stepped-refine-protein, stepped-refine-protein-for-rama) tp
be applied to a zone?  Please?

Cheers,

Ed.

PS.  Well, I was told long time ago that restraining Ramachandran
angles is a BAD idea because they should only be used for validation.
But this is 3A data.


-- 
Coot verendus est