On 1 Mar 2019, at 11:27, Brian Smith <[log in to unmask]> wrote:

Hi,

Wise words from Vicky.

You should always use the ARIA/CNS reported violations because they are the actual violations representing how CNS represents & uses the restraints. As it stands, analysis does not know how to read the structures and restraints back from ARIA in such a way that prochiral groups are treated correctly and (as far as I remember) it uses a catch all definition for these groups as a work around. That said, large violations will be reported by analysis.

Generally ARIA will reject any consistently violated (however that is defined in the iteration) restraints in each iteration and these can be found in the noe_restraints.violations table in each iteration directory. If you're getting ARIA to write the final restraints back into analysis, these will also be the REJECT list for each constraint list. I typically use these lists to find the problems in peak or restraint lists.

Brian

Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
          College of Medical, Veterinary & Life Sciences,
  Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
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From: CcpNmr software mailing list [[log in to unmask]] on behalf of Victoria Higman-Davies [[log in to unmask]]
Sent: 01 March 2019 10:13
To: [log in to unmask]
Subject: Re: violation in CCPNMR-STRUCTURE-RESTRAINTS AND VIOLATIONS

Hi Xiaowei,

I have had issues with Aria and CCPN giving me inconsistent/different violations. I think I came to the conclusion that this might be to do with Aria's floating chirality assignment - I have no idea whether CCPN takes this into consideration or not. Though I don't think I ever followed this up properly, so the issue may be different. The result is that I always use the Aria rather than the CCPN violation lists as they strike me as being more trustworthy. It is a nuisance and I have ended up with a Perl script that summarises my Aria violations and gives me a search string to find the violation in the CCPN restraint list. Then you can easily navigate to the peaks.

Vicky

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From: CcpNmr software mailing list <[log in to unmask]> on behalf of xiaowei CHEN <[log in to unmask]>
Sent: 01 March 2019 09:15:54
To: [log in to unmask]
Subject: Re: violation in CCPNMR-STRUCTURE-RESTRAINTS AND VIOLATIONS

 

Hi, Bruno

Yes, I checked the ARIA GUI. 
They are both activated.

Actually, there were violations in ccpnmr>restraints and violations after the first calculation. Then I corrected some according to the models and unambi.tbl/ambig.tbl.

Now, in CCPNMR, no violation, but when i check the models and unambig.tbl/ambig.tbl,  there are still a lot violations >0.2A.

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