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I would guess that it would be easier to restrain a helix by hydrogen bond lengths rather than by phi/psi torsion angles, and that could work for sheets as well. Phil On 8 Jan 2009, at 19:05, Garib Murshudov wrote: > If top/par file could be converted to the following type of > instructions then you do not need to define everything in cif file > (these are for torsion angles, all other restraints can be defined > similarly) > > General torsion angle restraints for any quartet of atoms: > > external torsion first chain [ch] residue [res] insertion [ins] > atom [n] [altecode [a]] next chain [ch] residue [res] insertion > [ins] atom [n] [altecode [a] ] [symm y/n] next chain [ch] residue > [res] insertion [ins] atom [n] [altecode [a] ] next chain [ch] > residue [res] insertion [ins] atom [n] [altecode [a] ] > [symm y/n] value <v> sigma <s> period> <p> > > Exampl > > external torsion first chain A residue 220 atom C next chain A > residue 220 atom CA next chain A residue 220 atom C next chain A > residue 221 atom N value -60 sigma 10 period 1 > > regards > Garib > > > > On 8 Jan 2009, at 18:14, Eckhard Hofmann wrote: > >> Hi Phil, >> sorry, haven't read you question properly. No idea how to get >> easily from top/par to cif for refmac..... >> Probably would need a little scripting, but that's been exactly >> your question ... >> Eckhard >> >> >> >> XPLO2D from the USF-Suite does this: >> >> <snippet from manual> >> You feed it a PDB file of the model to which you want to restrain >> your >> refinement model (e.g., that high-resolution native structure you >> already have, even though it may be in a different spacegroup or with >> different domain orientations). The program generates an X-PLOR >> include >> file which contains DIHEdral statements for the PHI, PSI, CHI-1 and >> CHI-2 torsions of the protein. If you protein contains a hinge >> region, >> simply remove or comment-out the relevant PHI and PSI restraints. >> If you >> don't want to impose restraints on CHI-1 and/or CHI-2, set the >> corresponding weights to zero (at the top of the X-PLOR include >> file). >> >> I never tried, but this will be compatible with phenix as well. >> Cheers >> Eckhard >> >> >> Phil Evans schrieb: >>> Does anyone have a good way of imposing secondary structure >>> restraints in a low resolution refinement? >>> I've done this in the past as hydrogen bond distance restraints >>> within helices, input to refmac as "LINK"s , with the list >>> generated with a little program and certain amount of pain >>> refmac now accepts an explicit list of external restraints, as >>> does phenix.refine, but I'm looking for a way of generating these >>> lists for quite a large structure without too much hackery, >>> perhaps from a hydrogen-bond or secondary structure assignment >>> program. Helices are reasonably straightforward (I can see how to >>> do them from eg DSSP), but sheets are more complicated. >>> Any suggestions? I'm sure that someone must have done this >>> Phil >> >> >> -- >> Eckhard Hofmann <[log in to unmask]> >> Ruhr-Uni Bochum >> AG Proteinkristallographie, LS Biophysik, ND04/316 >> 44780 Bochum >> Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 >>