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
