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In coot you have also the possibility to zoom into the ramachandran, this can
helps maybe.
Michel.
> Le 22 mars 2018 à 18:57, Ashley Pike a écrit :
>
> Running phenix.molprobity yourpdbfile from command-line used to work – will
> give a molprobity_coot.py (from which when you calculate>run sc
Running phenix.molprobity yourpdbfile from command-line used to work - will
give a molprobity_coot.py (from which when you calculate>run script in coot you
will get a clickable list of rama/rotamer outliers and clashes)
..although just checking it appears to not work with current COO
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You can evaluate your structure in MolProbity, then it would give a list of
Ramachandran outliers similar to the output of COOT.
http://molprobity.biochem.duke.edu/index.php?MolProbSID=ktiuaj4c1v48mlgqq3inopfrf6&eventID=22
Regards,
Burak
From: CCP4 bulletin
Hi Laurent,
I seem to recall being able to click on outliers in the output of the
phenix.refine GUI, which links to a Coot window. This would, however,
require refinement in the Phenix suite rather than the CCP4 one.
Best,
Chris
On Thu, Mar 22, 2018 at 10:27 AM, maveyrau
wrote:
> Hi all,
>
> I
Dear Laurant,
Perhaps not a complete answer to your question, but more of a strategy. You can
let the Ramachandran plot in COOT only show the outliers which would make
everything a bit more tangible. Then only go for the massive outliers, these
are the problems that need rebuilding (e.g. throug
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Hi all,
I’m currently refining quite a big oligomer (about 3500 residues) using
refmac/coot, at a 2.85 A resolution. The Ramachandran tool in Coot indicates
about 100 outliers, and I would like to check them individually… Is there a way
to get a clickable list of outliers? I know I can click o
Hi Manoj
As regards the HKL .sca file, it depends on what type of .sca file it is -
there are two types, one which has the reflections merged into unique
reflections (so, for example, there will be one entry for the (-8 5 6)
reflection) and the other which does not have the equivalent reflectio
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