[ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #2

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

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On Thursday 01 November 2001 09:34, I wrote:

> I am having many problems in trying to describe new ligands for use in
> refmac5 refinement. The problem is that if refmac5 finds some monomer in the
> standard libraries that looks vaguely similar to mine, it insists on using
> that one instead of the one I explicitly specified.  Is there some way to
> tell it _not_ to second guess my choice of descriptions?

Thanks to many people who pointed out the MAKE CHECK NONE option
for refmac5. That handles problem #1.

Now for a follow-on problem.  I ended up heavily editing the monomer library
file for my ligand because the ccp4i chemistry sketcher fails to capture the
geometry correctly. At this point I am not so much worried about this particular 
ligand; I just want to learn how to use the sketcher to generate new monomer libraries.

The ligand has multiple 6-membered rings.  One of these is aromatic, and hence 
planar, while two are saturated.

Scenario 1:

1) In the sketcher I read in a PDB file containing coordinates with externally
    idealized geometry but with no hydrogens.
2) I attempt to edit the planarity restraint list, but nothing I do seems to be
    saved in the monomer library I am about to write.  Instead it makes up its
    own (incorrect) restraints.
3) I tell the sketcher to create a new monomer library containing this structure.
    I selected options: "extract ideal geometry from coordinates" and
    "load and display hydrogen atoms"
4) The resulting library correctly handles one of my rings (aromatic).
     For one of the saturated rings (ideal chair in input file) it assigns aromatic
     chemical types, resets the target geometry to 120 degree angles,
     generates planarity restraints, and adds hydrogens as if it were aromatic.  
     For the other saturated ring (a pyranose sugar) it assigns aromatic
     chemical types, leaves the geometry alone, generates planarity restraints,
     and adds no hydrogens at all.

Scenario 2:

1) Same coordinate file input, but this time I use the sketcher to add explicit
    hydrogens.
2) Again editing or not editing  the planarity restraint list seems to make no
    difference.
3) When I create a library description things are a bit better than before, 
    but it still creates incorrect planarity restraints and this time the connectivity 
    list for the second saturated ring is a bit strange.  
    This was the file I hand-edited and eventually used for refmac5 

Any suggestions as to what I should do differently?   

Why does it insist on making my saturated rings planar?  When I edit the
planarity restraints interactively, how do I make it keep the new ones in 
the created library file?

Why does it fail in two different ways on the two different saturated rings, in
one case taking the geometry from the coordinate file but in the other case not?

Is it generally required to add all hydrogens in order to get a half-way correct
library generated?

p.s.
By the way - despite these problems, I really like the sketcher tool!


-- 
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