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Re: [ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #4
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Dear Ethan,
Yes. At the moment refmac ignores all torsion angles apart form those for amino
acids (as you have already spotted chi_XXX
and/or omeg_XXX). I am adding option to restraint given restraints by residue and
torsion angle names.
It will be in the next version.
And for anomers 'both' should be used. But in version 5.0.xx sugars will not be
treated as sugars (I.e. they will not make
standard sugar links unless you define specific links for them. in 5.1 they are
treated as sugar with all standard links. sugar-sugar
and/or sugar-protein).
regards
Garib
Ethan Merritt wrote:
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> On Monday 05 November 2001 14:04, I wrote:
>
> >Problem #3
> > As best as I can make out, refmac5 is totally ignoring any torsion angle
> > restraints in my private monomer library files.
>
> I plunged into the refmac5 code and emerged again with enthusiasm only
> slightly dampened.
>
> Yes indeed, refmac5 ignores all torsion restraints for torsion angles that
> are not explicitly named "chiXXX" or "omegXXX".
> Since the torsion descriptions created by the library tools are named
> "var_xxx" or "CONST_xxx", they are ignored.
>
> Quick fix:
> I renamed torsion angles in my monomer library to be "chi_XXX"
>
> Proposal for better fix:
> I could remove the naming restriction in refmac5, but that would
> break the existing behaviour for all the standard libraries. Ugh.
> Probably better to add an option to the library tools (libcheck,
> ccp4i sketcher, etc); if you select the option then it names the
> torsion angles "refinable_XXX" instead of "var_XXX". Then refmac5
> can be changed to pay attention to "refinable" torsions in addition
> to chi and omega.
>
> The refmac code change would be trivial.
> Changing the ccp4i sketcher is another question, since I'm not a Tk/Tcl hacker.
>
> Comments?
>
> > Problem #4
> > I have a sugar which is present as an anomeric mixture of the alpha- and
> > beta- anomer forms. How do I describe this to refmac5?
>
> This turns out to be an undocumented feature already, or at least I cannot
> find it anywhere in the documentation.
>
> The legal values for _chem_comp_chir.volume_sign are
> "posi" "nega" "both"
>
> Just what I wanted :-)
>
> --
> Ethan A Merritt merritt@u.washington.edu
> Biomolecular Structure Center Box 357742
> University of Washington, Seattle, WA 98195
> phone: (206)543-1421
> FAX: (206)685-7002
--
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Garib N. Murshudov, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 62 87, work: +44 (1904) 43 25 65
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