Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

[C]

Isn't Molprobity too tight anyway for high resolution structures? 

I have often (for proteins) found it highlighting "outliers" when in fact that is what the density shows.

Isn't it a trade off between molprobity and what the measurements show, especially at high resolutions?

-----Original Message-----
From: merr...@u.washington.edu
Sent: Mon, 15 Sep 2014 08:35:37 -0700
To: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote:

> Does anyone know if Molprobity has recently changed the standard bond lengths and angles that it uses ?

>

> Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new structure refined with Refmac. I then tried Molprobity on a deposited PDB structure that also contains AMPPNP and it reported the same errors. I am sure that these errors were not reported when this structure (2JDI) was deposited in 2007.

>

> This would suggest that the standard dictionary that Molprobity uses has changed, but I cannot find any reference to this on the Molprobity pages.

>

> I would be very grateful if anyone can throw some light on this.

 

I suspect, though I cannot say for sure, that the difference is

whether ANP is [correctly] treated as a ligand or [incorrectly]

treated as a monomer in a nucleic acid polymer. We have seen

similar cases recently. For now I would say it is safe to

disregard Molprobity scores for ligands that just happen to be

nucleic acids.

 

Ethan

 

 

 

 

> Thanks,

>

> Andrew

 

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