Re: [COOT] Coot and D-amino acids

[Paul Emsley]

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 
 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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Re: [COOT] Coot and D-amino acids

[prasun kumar]

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.

Cheers
Prasun
[image: image.png]

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success


On Wed, Nov 3, 2021 at 10:41 PM Paul Emsley 
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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Re: [COOT] Coot and D-amino acids

[Paul Emsley]

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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[COOT] Coot and D-amino acids

[prasun kumar]

Hi All:

I have a structure that has a lot of D-amino acids. When I open the mtz and
pdb it shows me C-beta outlier warning (Molprobity Warnig). I have also
downloaded D-amino acids peptides and corresponding mtz files from the PDB
and got similar warnings.
Can you please guide me how to get rid of it?


Cheers
Prasun
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success



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