search

MonomerLibrary / monomers

dictionary of monomers and links
GNU Lesser General Public License v3.0
13 stars 85 forks source link

Starting coordinates and restraints for HEO #36

Open drlemmus opened 10 months ago

drlemmus commented 10 months ago

This came up at the Cold Spring Harbor Course for crystallography: the starting coordinates for HEO are pretty garbled. They clean up quite nicely when you idealise the coordinates, but the iron gets pouched out of the plane.

keitaroyam commented 10 months ago

It perhaps became a seasonal tradition.. https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2210&L=CCP4BB&P=R104954 Of course we should fix it. Some were fixed after this ccp4bb post by the way: https://github.com/MonomerLibrary/monomers/pull/8

GaribMurshudov commented 10 months ago

I think we need to sort out all heam like structures. There are errors in them in CCD (e.g. HEO, atom NB and ND have +1 charge on them. They also have double and single bonds. If this would be like that then FE would fly. On the other hand NB and NC are neutral. These problems cause additional problems. I think all heam like structures (around 66 of them) should be checked and update in our monomer library and in the CCD. (SRM was just one of the problems which pdb has not correted yet)