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
RD, 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 PAd 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 PCd 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
