> But I feel that this is a something of a proxy for the original question > (which I took to be "show me NCS related residues that have side-chains in > different rotamers").
Yes, a Kleywegt plot for side chain rotamers. Possibly with the option to look just at hydrophobic or polar residues. Rotamer differences in poorly ordered, solvent-exposed polar side chains might not matter, but different rotamers in in the hydrophobic core of the protein probably mean a modelling mistake. Luca > The scripting function of interest in Coot is get-rotamer-name, but there is > no function provided to run this over a pair of chains and compare results. > > Paul. > > On 20/06/12 11:24, Eleanor Dodson wrote: >> If you use the " superpose molecules" task, using LSQKAB , and fit molecule >> A over molecule B say, asking for all atoms to be fitted, you will get a >> list of large deviations for main and side , which should include all those >> residues with side chains in different rotamers. >> >> Eleanor >> >> On 20 June 2012 10:22, Antony Oliver <[email protected]> wrote: >> <forgive the cross-posting coot-bb/ccp4-bb> >> >> Can I second that please? I am possibly in a similar situation - >> 2.8 Angstrom structure, 6 molecules in the asymmetric unit, refining with >> ncs torsion restraint. >> It would be very useful to identify which side-chains are in different >> rotamers (without having to look at each and every side-chain). >> >> Tony. >> >> --- >> Dr Antony W Oliver >> >> Senior Research Fellow >> CR-UK DNA Repair Enzymes Group >> Genome Damage and Stability Centre >> Science Park Road >> University of Sussex >> Falmer, Brighton, BN1 9RQ >> >> email: [email protected] >> tel (office): +44 (0)1273 678349 >> tel (lab): +44 (0)1273 677512 >> >> >> >> >> On 6/20/12 10:04 AM, "Luca Pellegrini" <[email protected]> wrote: >> >> >Hello, >> > >> >Is there a way to flag up residues that have been modelled with different >> >side chain rotamers in two NCS-related molecules? I can use the NCS Ghost >> >Control tool to check individual residues but it would be useful to be >> >able to produce a list, so that one can zoom in on possible outliers. >> > >> >Thanks, >> >Luca >> > Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
