Dear colleagues, I'm having an issue with a particular ligand in JLigand 1.0.40. When I load NRQ, the topology is correct but the bond lengths and angles are highly distorted, making it uninterpretable to my eye. A screenshot is viewable at https://www.dropbox.com/s/44nmmc96899o3uo/NRQ.tiff?dl=0.
If I make some edit to the molecule and then regularize it, everything looks fine. I have not found another ligand with similar behavior. In an older version (1.0.37), this does not happen. On the machine with JLigand 1.0.40 (aberrant behavior), I have: CCP4 software suite: library version 6.5.008 CCP4 software suite: patch level 6.5.008 Program: refmac5; version 5.8.0107 --- LIBCHECK --- /Vers 5.2.02 ; 02.12.2014/ dictionary version 5.44 On the machine with JLigand 1.0.37 (normal behavior), I have: CCP4 software suite: library version 6.5.008 CCP4 software suite: patch level 6.5.008 Program: refmac5; version 5.8.0107 --- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/ dictionary version 5.44 Best wishes Kevin Jude
