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
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