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What's interesting to me is that it's only the protons that are moving. I observe protein drift in Aria 2.2/2.3, but it's always the whole molecule. What do the structures look like? Are the heavy atoms ok? What iteration is this, etc? Are the protons in the structures that aren't out of range still far from their heavy atoms? Any errors in the log files? The energetics of these structures should be horrible. Regards, David ----------------------------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: [log in to unmask] web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -----Original Message----- From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Paul Driscoll Sent: Tuesday, April 06, 2010 1:26 PM To: [log in to unmask] Subject: Re: Weird coordinates in pdb I am not an expert with Aria, just basing my comments on (long) past experience: Maybe its just a 'bad' structure. The **** probably means that the atoms have gone outside the normal recordable range (at least in a PDB file) meaning that they somehow got too hot and just went shooting off. If your other structures are sensible then I would put this down to bad luck. If not, then you need to find out what is conflicting what, change the annealing schedule, etc... Paul Quoting Justin Lecher <[log in to unmask]>: > Dear all, > > I am running a aria/cns run and getting weird coordinate ouputs: > > REMARK DATE:06-Apr-2010 17:00:01 created by user: justin > REMARK VERSION:1.21 > ATOM 1 HA1 GLY 1 566.791********-334.675 1.00 0.00 A > ATOM 2 HA2 GLY 1 569.400********-331.640 1.00 0.00 A > ATOM 3 C GLY 1 -8.712 -14.245 -1.246 1.00 0.00 A > ATOM 4 O GLY 1 -11.456 -15.723 1.311 1.00 0.00 A > ATOM 5 N GLY 1 -8.348 -20.275 -1.520 1.00 0.00 A > ATOM 6 HT1 GLY 1 1309.5112360.255-991.878 1.00 0.00 A > ATOM 7 HT2 GLY 1 1306.8152362.990-992.513 1.00 0.00 A > ATOM 8 HT3 GLY 1 1304.8262359.182-991.768 1.00 0.00 A > ATOM 9 CA GLY 1 -9.816 -18.030 -0.664 1.00 0.00 A > ATOM 10 N ALA 2 -9.148 -13.887 -3.596 1.00 0.00 A > ATOM 11 HN ALA 2 ****************1114.891 1.00 0.00 A > ATOM 12 CA ALA 2 -7.448 -12.306 5.452 1.00 0.00 A > ATOM 13 HA ALA 2 ****************1472.573 1.00 0.00 A > ATOM 14 CB ALA 2 -8.305 -14.055 1.779 1.00 0.00 A > ATOM 15 HB1 ALA 2 853.470 886.716******** 1.00 0.00 A > ATOM 16 HB2 ALA 2 849.706 891.587******** 1.00 0.00 A > ATOM 17 HB3 ALA 2 856.669 893.961******** 1.00 0.00 A > ATOM 18 C ALA 2 -8.626 -14.930 2.929 1.00 0.00 A > ATOM 19 O ALA 2 -9.001 -12.827 -2.662 1.00 0.00 A > ATOM 20 N MET 3 -5.648 -11.922 -4.334 1.00 0.00 A > ATOM 21 HN MET 3 ****************1329.466 1.00 0.00 A > ATOM 22 CA MET 3 -4.870 -11.907 -4.598 1.00 0.00 A > ATOM 23 HA MET 3 ****************1350.969 1.00 0.00 A > > This happens in two of ten calculated structures. Does anbody know > where this comes from, or how to fix that? > > Thanks justin > > > -- > Justin Lecher > Institute for Neuroscience and Biophysics ISB 3 - Institute for > structural biochemistry Research Centre Juelich GmbH, > 52425 Juelich,Germany > phone: +49 2461 61 5385 > > > -- Paul C. Driscoll Honorary Professor of Structural Biology Structural and Molecular Biology University College London Gower Street London WC1E 6BT, UK Tel.: 44-20 7679 7035 Mobile: 07876 777937 ------------------------------------------------- This mail sent through UCL Biochemistry's Webmail: http://webmail.biochem.ucl.ac.uk/ (unsecured) https://webmail.biochem.ucl.ac.uk/ (secured)