Re: [ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #4

[Ethan Merritt <merritt@u.washington.edu>]

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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