ideal MG-oxygen distances in refmac

From: Gregory Bowman
Date: 27 February 2012 17:06

Hi all,

I'm building a ~1.9Å structure that has a few Mg++ ions bound. I thought that the expected distance for Mg-O was 2.1Å, but in refmac the default to Asp/Glu oxygens appears to be 1.91 Å. Strangely, for a Mg-bound pyruvate ligand, the default distance to one oxygen is 2.18 Å, but 1.91 Å for the other:

= = = (from log file)

 I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.006 ideal_dist=   1.910
            ch:AA   res: 272  GLU      at:OE1 .->ch:Ab   res: 601  MG       at:MG  .
  INFO:     link is found (not be used) dist=   1.943 ideal_dist=   1.910
            ch:AA   res: 296  ASP      at:OD2 .->ch:Ab   res: 601  MG       at:MG  .
  INFO:     link is found (not be used) dist=   1.853 ideal_dist=   1.910
            ch:Ab   res: 601  MG       at:MG  .->ch:Ac   res: 602  PYR      at:O2  .
  INFO:     link is found (not be used) dist=   2.061 ideal_dist=   2.180
            ch:Ab   res: 601  MG       at:MG  .->ch:Ac   res: 602  PYR      at:O3  .
  INFO:     link is found (not be used) dist=   2.076 ideal_dist=   1.910
            ch:BB   res: 272  GLU      at:OE1 .->ch:Bb   res: 601  MG       at:MG  .
  INFO:     link is found (not be used) dist=   2.045 ideal_dist=   1.910

= = =

What's the easiest way to change this default distance - altering a file in the monomer libraries or explicitly stating the LINK distances? I'm using refmac version 5.6.0117 in ccp4 6.2.0 on MacOS 10.6.8. 

Thanks,

Greg