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
>>
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