[ccp4bb]: Refmac standard ligand libraries

["Frank Vondelft" <Frank.Vondelft@syrrx.com>]

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Hi all

We happened across TMP (thymidine monophosphate) in some random
structure, and after building it, I blithely launched refmac (ccp4
v4.2.1) without bothering to create a ligand definition, and telling it
not to make one either, since I saw that TMP had been defined in the
standard refmac library ($CBLID_MON).  Much to my puzzlement, refmac
crapped out telling me that oft featured message, that it only had a
minimal ligand description and had helpfully created one for me and I
should restart it etc etc. 

Of course I went and meticulously compared atom names, pdb formatting,
all the usual culprits, but still refmac would not see it.  Finally I
created the thing with library sketcher and now refmac ran, of course. 

Upon comparing the entry in the standard library with that from
libcheck, I noticed that the standard library defines only atoms and
bond lengths, while libcheck included the other stuff (angles, planes,
torsions) too.  I further noticed that the standard library for ATP
(which *is* automatically recognized) *does* contain angles, planes and
torsions.  Finally, I saw that there are a great many ligands that are
"incompletely" defined.  

Question:  since refmac appears to require full definitions, is this a
bug in refmac, or a bug in the standard library? 

cheers
phx.


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