Dear Users: The problem is as old as the introduction of floating chirality, as information is lost in the transfer between different programs! Fortunately, this issue is solved by adoption of the NEF for exchanging restraints and mmCIF for structures. We are actually organising in the coming months a round-robin between all key-developers as a test of this principle. I realise that this does not fix your immediate problem; the analysis of the original program (as it has access to all the ‘data’) is the one to use. In the AnalysisStructure version-3 (currently under development) we will be fully compliant with with NEF/mmCIF and its analysis routines will therefore be good for these cases. Best Geerten ------------------------------------------------------------------------------------- Prof. Geerten W. Vuister Chair in Structural Biology Chair of Collaborative Computational Project for NMR (CCPN) Department of Molecular and Cell Biology Leicester Institute of Structural and Chemical Biology University of Leicester Henry Wellcome Building, Lancaster Road Leicester, LE1 9HN, United Kingdom Phone: +44 116 229 7076 Email: [log in to unmask]<mailto:[log in to unmask]> http://www2.le.ac.uk/departments/molcellbiol http://www.ccpn.ac.uk On 1 Mar 2019, at 11:27, Brian Smith <[log in to unmask]<mailto:[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. Tel: 0141 330 5167/6459/3089 ---------------------------------------------------------------------- The University of Glasgow, charity number SC004401 ________________________________ From: CcpNmr software mailing list [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Victoria Higman-Davies [[log in to unmask]<mailto:[log in to unmask]>] Sent: 01 March 2019 10:13 To: [log in to unmask]<mailto:[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 ________________________________ From: CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]>> on behalf of xiaowei CHEN <[log in to unmask]<mailto:[log in to unmask]>> Sent: 01 March 2019 09:15:54 To: [log in to unmask]<mailto:[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. ######################################################################## To unsubscribe from the CCPNMR list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCPNMR%26A%3D1&data=02%7C01%7Cgv29%40LEICESTER.AC.UK%7C756ef4764e57475e796a08d69e38f3d5%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636870364790162919&sdata=WWRs0lQiALXlTDQXS0L1U9fPj2b1jPRUyprThjCCRPI%3D&reserved=0> ________________________________ To unsubscribe from the CCPNMR list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCPNMR%26A%3D1&data=02%7C01%7Cgv29%40LEICESTER.AC.UK%7C756ef4764e57475e796a08d69e38f3d5%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636870364790172924&sdata=A1M4VrxZF1qfPcChNsqtjMbZvKFjdCZBO95b1Jd54YU%3D&reserved=0> ________________________________ To unsubscribe from the CCPNMR list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCPNMR%26A%3D1&data=02%7C01%7Cgv29%40LEICESTER.AC.UK%7C756ef4764e57475e796a08d69e38f3d5%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636870364790172924&sdata=A1M4VrxZF1qfPcChNsqtjMbZvKFjdCZBO95b1Jd54YU%3D&reserved=0> ######################################################################## To unsubscribe from the CCPNMR list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1