Re: [ccp4bb]: REFMAC library

[Garib Murshudov <garib@ysbl.york.ac.uk>]

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>

Refmac uses links (by default) if user defines it in his pdb file using
LINK record. Otherwise it
anylises and says you may have but does not use. You can run refmac with

MAKE LINK YES

then it will create link record in your pdb and corresponding dictionary
entry and exit. Then you can play
with pdb and dictionary

Garib

>
>
> >From a REFMAC5 run I get a list of INFOs like the sample below:
>
>   I am reading library. Please wait.
>                 mon_lib.cif
>   INFO:  connection is found (not be used) dist= 1.325 ideal_dist= 1.330
>             ch:AA res: 405 GLY at:C --> ch:Aa res: 406 CYP at:N
>   INFO:  connection is found (not be used) dist= 2.324 ideal_dist= 2.300
>             ch:AA res: 312 CYS at:SG --> ch:Cc res: 710 FE6 at:FE6
>
> I've checked and it makes sense for my protein but I didn't set those
> links in dictionary (telling the trued because I don't know how). I was
> happy to "see" that REFMAC could understand that connections existed but
> my happiness went away when I saw the "not be used"...
>
> Is it any fast way of telling it to use this links ?
>
> David Aragao
> Linux User nš 237333 on http://counter.li.org/
>
> "For every complex problem there is an answer that is clear, simple,
> and wrong."
>         - H. L. Mencken (1880-1956)
>
> P.S: CYP is a persulphide-Cysteine that I've created.

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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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