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 >
