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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 >