On 15 September 2014 17:48, Ian Tickle wrote:
>
>
> ANP C5 C4 C3 126.8 0.7
>
> Oops sorry, typo:
>
ANP C5 C4 N3 126.8 0.7
I.
On 15/09/14 18:05, Dale Tronrud wrote:
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On 9/15/2014 9:42 AM, Andrew Leslie wrote:
Dear Huw,
Many thanks for this information. I had seen the notice about
Molprobity using CCTBX validation metrics, but I mistakenly thought
that Phenix used the CCP
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On 9/15/2014 9:42 AM, Andrew Leslie wrote:
> Dear Huw,
>
> Many thanks for this information. I had seen the notice about
> Molprobity using CCTBX validation metrics, but I mistakenly thought
> that Phenix used the CCP4 monomer library, which I think
Andrew, GRADE gives:
ANP C5 C4aromatic 1.388 0.011
ANP C5 C4 C3 126.8 0.7
i.e. essentially the same as Phenix, so I would go with that.
The CCP4 values definitely could do with a re-examination: I've never heard
of a "double bond" with a length of 1.49, an
Dear Huw,
Many thanks for this information. I had seen the notice about Molprobity using
CCTBX validation metrics, but I mistakenly thought that Phenix used the CCP4
monomer library, which I think was true once but is clearly no longer the case.
Given the very small sigma values associated wit
On 15 Sep 2014, at 15:24, Andrew Leslie wrote:
> 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
: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 lengt
Hi Andrew,
the ccp4 ANP.cif entry for C4'-C5' is 1.528A, but both the Phenix and
Grade cif list 1.508A. The distance in 2JDI is 1.53, so if molprobity
relies on one of the latter two sources, this might be the source of the
flag. Also some shelxl dictionary lists 1.509A, so it's 3:1 for the flag
b
utions?-Original Message-From: merr...@u.washington.eduSent: Mon, 15 Sep 2014 08:35:37 -0700To: ccp4bb@jiscmail.ac.ukSubject: 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 h
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 AMP
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