Hi Robbie OK I just realised what's going on. In my script I renumber the input PDB file (starting at 1 for each chain and incrementing by 1) and keep the mapping so I can renumber it back afterwards for human consumption. So you're completely correct: there is indeed a residue A59 after renumbering! This is to avoid headaches with brain-damaged programs that can't cope with insertion codes and residue numbers out of sequence. So I guess I'm going to have to be smarter in my renumbering program and make sure I maintain any increasing gaps in the numbering which indicate real gaps in the sequence and only renumber over insertions and decreasing gaps. It doesn't actually matter what the new numbers are since the user never sees them.
But this must be a common problem: how do others handle this? E.g. pdbset blindly renumbers with a increment of 1 (and anyway it doesn't renumber any LINK, SSBOND & CISPEP records as I do) so it would have the same problem. Cheers -- Ian On 18 February 2013 17:09, Robbie Joosten <[email protected]>wrote: > Hi Ian, > > The warning refers to a MET 59 in chain A whereas you only have MET 72. > That > is very suspicious. Non-sequential residues further apart than x Angstrom > automatically get a gap record. Have you tried a newer version of Refmac, > because this feature was added quite a while ago? > What is your setting for 'MAKE CONN' when you run Refmac? > > Cheers, > Robbie > > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > > Ian Tickle > > Sent: Monday, February 18, 2013 17:32 > > To: [email protected] > > Subject: [ccp4bb] Link problem with Refmac. > > > > > > All, I'm having a problem with Refmac (v. 5.7.0025) that I don't > understand. > > It's linking 2 residues that it shouldn't be. Here's the relevant > message > in the > > log file: > > > > WARNING : large distance for conn:TRANS dist = 10.768 > > ch:AA res: 58 THR --> 59 MET > ideal_dist= 1.329 > > > > Note that there are no LINK (or LINKR) records in the PDB header. > > > > > > Here are the input co-ords for the relevant residues (not linked): > > > > ATOM 887 N THR A 58 13.587 1.365 19.814 1.00 14.28 A > N > > ATOM 888 CA THR A 58 14.743 1.126 18.960 1.00 17.64 A > C > > ATOM 890 CB THR A 58 14.325 0.613 17.567 1.00 17.69 A > C > > ATOM 892 OG1 THR A 58 13.605 1.650 16.879 1.00 15.24 A > O > > ATOM 894 CG2 THR A 58 13.505 -0.658 17.658 1.00 17.33 A > C > > ATOM 898 C THR A 58 15.573 2.346 18.631 1.00 22.80 A > C > > ATOM 899 O THR A 58 15.144 3.492 18.842 1.00 20.41 A > O > > ATOM 956 N MET A 72 13.605 -6.845 13.378 1.00 43.23 A > N > > ATOM 957 CA MET A 72 12.268 -6.980 12.733 1.00 39.06 A > C > > ATOM 959 CB MET A 72 12.308 -6.361 11.331 1.00 42.06 A > C > > ATOM 962 CG MET A 72 12.455 -4.846 11.320 1.00 43.45 A > C > > ATOM 965 SD MET A 72 13.020 -4.153 9.755 1.00 46.07 A > S > > ATOM 966 CE MET A 72 14.695 -4.789 9.653 1.00 49.84 A > C > > ATOM 970 C MET A 72 11.544 -8.344 12.624 1.00 36.94 A > C > > ATOM 971 O MET A 72 10.314 -8.353 12.558 1.00 34.24 A > O > > > > > > Here are the same residues (linked) after refinement: > > > > ATOM 887 N THR A 58 14.212 0.104 18.340 1.00 43.09 A > N > > ATOM 888 CA THR A 58 14.332 -1.166 17.541 1.00 45.12 A > C > > ATOM 890 CB THR A 58 12.906 -1.657 17.309 1.00 39.26 A > C > > ATOM 892 OG1 THR A 58 12.400 -1.039 16.117 1.00 38.40 A > O > > ATOM 894 CG2 THR A 58 12.010 -1.301 18.435 1.00 33.96 A > C > > ATOM 898 C THR A 58 14.805 -1.376 16.064 1.00 59.98 A > C > > ATOM 899 O THR A 58 15.304 -0.470 15.386 1.00 69.73 A > O > > ATOM 901 N MET A 72 14.609 -2.641 15.623 1.00 61.67 A > N > > ATOM 902 CA MET A 72 13.990 -2.997 14.308 1.00 60.32 A > C > > ATOM 904 CB MET A 72 14.898 -2.730 13.093 1.00 71.29 A > C > > ATOM 907 CG MET A 72 14.126 -2.345 11.812 1.00 73.22 A > C > > ATOM 910 SD MET A 72 12.912 -3.499 11.087 1.00 69.42 A > S > > ATOM 911 CE MET A 72 13.917 -4.503 9.996 1.00 63.68 A > C > > ATOM 915 C MET A 72 13.413 -4.438 14.205 1.00 59.57 A > C > > ATOM 916 O MET A 72 12.199 -4.599 14.130 1.00 60.33 A > O > > > > > > Residues 59-71 are present but in a poorly defined loop so I definitely > do > not > > want residues 58 & 72 linked! I'm puzzled because I'm sure it never used > to > > do this, i.e. you had to specify a LINK if you wanted one and Refmac was > > smart enough to recognise that residues across a break should not be > linked. > > So how do I tell it NOT to link them? > > > > > > Cheers > > > > > > -- Ian > > >
