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

 

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.

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Robbie Joosten
Sent: 27 January 2013 13:27
To: [log in to unmask]
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: [log in to unmask]
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