Yes, a good pdb converter jiffy that picks up and corrects/highlights differences and errors in the atom name from the residue name would be great to have. I’m using pdbvconv from Global Phasing which is pretty good. It gets a little confused when the atoms names are a mixture of pdbv2 and v3. This has happened with NAD which a couple of times,
Jon Read Associate Principal Scientist _____________________________________________________________________ Astrazeneca R&D, Decs, Astrazeneca, Mereside, Alderley Park, Cheshire, SK10 4TG UK Tel +44 (0)1625 510661 Mobile +44 (0)7775 040376 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: 27 January 2013 13:27 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] edit chi angles of DNA in coot Hi Lisa, I'm not sure it's the source of your problem, but your atom names are still in PDBv2 format. That's 'so last decade'. Start by fixing that. There must be a CCP4 tool that will do that. You can also use the MolProbity server to fix the format. For the developers: the problem with atom and residues in the old naming scheme is really annoying. Are there still programs that write this? Perhaps support for the PDBv2 should be dropped by now except in a few format converters. Cheers, Robbie Sent from my Windows Phone ________________________________ From: LISA Sent: 2013-01-27 13:19 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] edit chi angles of DNA in coot Hi all, I am refining a protein-DNA complex. But when I adjust the position of DNA by "edit chi angels", the phosphate does not move. Only the sugar and base move Here is partial DNA pdb. Is there any format problem of my pdb or I miss some library? ATOM 10825 P Ad D 11 17.140 11.607 42.723 1.00 29.20 P ATOM 10826 O1P Ad D 11 16.898 12.582 41.641 1.00 29.72 O ATOM 10827 O2P Ad D 11 18.154 11.916 43.743 1.00 33.07 O ATOM 10828 O5* Ad D 11 17.537 10.169 42.137 1.00 31.19 O ATOM 10829 C5* Ad D 11 17.790 9.108 43.047 1.00 25.02 C ATOM 10830 C4* Ad D 11 17.956 7.803 42.314 1.00 30.93 C ATOM 10831 O4* Ad D 11 16.670 7.304 41.858 1.00 29.79 O ATOM 10832 C1* Ad D 11 16.870 6.713 40.601 1.00 36.62 C ATOM 10833 N9 Ad D 11 15.636 6.710 39.824 1.00 33.20 N ATOM 10834 C8 Ad D 11 14.968 7.801 39.371 1.00 22.90 C ATOM 10835 N7 Ad D 11 13.896 7.505 38.680 1.00 26.56 N ATOM 10836 C5 Ad D 11 13.870 6.121 38.654 1.00 31.80 C ATOM 10837 C4 Ad D 11 14.942 5.617 39.358 1.00 32.61 C ATOM 10838 N3 Ad D 11 15.238 4.325 39.551 1.00 27.80 N ATOM 10839 C2 Ad D 11 14.334 3.546 38.961 1.00 27.51 C ATOM 10840 N1 Ad D 11 13.252 3.882 38.250 1.00 21.29 N ATOM 10841 C6 Ad D 11 12.980 5.187 38.073 1.00 31.66 C ATOM 10842 N6 Ad D 11 11.890 5.516 37.368 1.00 29.64 N ATOM 10843 C2* Ad D 11 17.929 7.576 39.923 1.00 36.75 C ATOM 10844 C3* Ad D 11 18.836 7.949 41.084 1.00 36.29 C ATOM 10845 O3* Ad D 11 19.919 7.056 41.170 1.00 37.96 O ATOM 10846 P Cd D 12 21.191 7.246 40.214 1.00 55.12 P ATOM 10847 O1P Cd D 12 22.397 7.328 41.071 1.00 49.33 O ATOM 10848 O2P Cd D 12 20.886 8.343 39.272 1.00 47.47 O ATOM 10849 O5* Cd D 12 21.226 5.885 39.374 1.00 51.47 O ATOM 10850 C5* Cd D 12 21.346 4.667 40.093 1.00 49.75 C ATOM 10851 C4* Cd D 12 20.769 3.488 39.334 1.00 39.32 C ATOM 10852 O4* Cd D 12 19.343 3.656 39.226 1.00 32.96 O ATOM 10853 C1* Cd D 12 18.882 2.909 38.120 1.00 30.55 C ATOM 10854 N1 Cd D 12 17.966 3.801 37.377 1.00 31.81 N ATOM 10855 C2 Cd D 12 16.867 3.239 36.734 1.00 24.72 C ATOM 10856 O2 Cd D 12 16.717 2.019 36.807 1.00 32.01 O ATOM 10857 N3 Cd D 12 16.011 4.047 36.070 1.00 23.04 N ATOM 10858 C4 Cd D 12 16.243 5.365 36.022 1.00 28.69 C ATOM 10859 N4 Cd D 12 15.377 6.135 35.351 1.00 18.23 N ATOM 10860 C5 Cd D 12 17.370 5.958 36.668 1.00 27.01 C ATOM 10861 C6 Cd D 12 18.198 5.145 37.329 1.00 28.78 C ATOM 10862 C2* Cd D 12 20.104 2.429 37.341 1.00 34.57 C ATOM 10863 C3* Cd D 12 21.222 3.310 37.890 1.00 31.03 C ATOM 10864 O3* Cd D 12 22.469 2.619 37.840 1.00 34.98 O -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
