On 03/11/2021 23:22, prasun kumar wrote:
Sorry Paul for not putting it more clearly.
After running Refmac5 from CCP4i2, I open the mtz file and pdb in
COOT. There I get a warning message (Picture attached). I can get this
off if I turn off the run Molprobity option in CCP4i2. I was just
wondering if I can get any clue to handle this warning in Coot. Or, I
should not bother about it.
Well, these results are not created by Coot, Coot is merely being used
to provide an interactive table.
For what it's worth, the results are (without looking at the structure),
to me, somewhat eyebrow raising.
You can indeed get a Coot-based handle on these results. The "Overlaps,
Peptides, C-betas, Rama & Rotas" menu item in Validate will inform you
about what Coot thinks about C-Beta outliers (and other things
obviously). However, Coot doesn't use the dictionary to check the
chirality of the residue before generating an ideal position for the CB
(I should fix that) so I guess that it will make the same mistake that
molprobity does.
You may need to install this script from CURLEW.
Paul.
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
On Wed, Nov 3, 2021 at 10:41 PM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk> wrote:
On 03/11/2021 22:28, prasun kumar wrote:
>
>
> I have a structure that has a lot of D-amino acids. When I open the
> mtz and pdb
open it in Coot you mean?
> it shows me C-beta outlier warning (Molprobity Warnig).
Coot doesn't do that. Are you talking about some other program?
> I have also downloaded D-amino acids peptides and corresponding mtz
> files from the PDB and got similar warnings.
I don't follow what you're doing. Coot doesn't run molprobity C-beta
analysis (it has its own).
Paul.
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