On 17/05/2019 17:10, Hannah Bridges wrote: > > > I am using coot 0.9-pre (ccp-em) with a protein that contains Fe-S > clusters. Although the bonds are now drawn between the Fe and S atoms > (thanks Paul!) and the clusters no longer explode when you real space > refine without adding your own restraints, when you do real space > refine in coot, the default settings appear to make the 4Fe-4S > clusters pretty much cubic. > > A recent article by Nigel Moriarty and Paul Adams has looked at all > the hi-res pdb structures with FeS clusters and found out the average > angles: > > https://onlinelibrary.wiley.com/iucr/doi/10.1107/S205979831801519X
Yes, that was interesting. > > I was wondering if it would be possible for the coot default > restraints to be updated to reflect this? If not we will just continue > adding our own restraints, but there may be people out there who don't > know that their 4Fe-4S cluster isn't supposed to be a cube! > Coot uses the CCP4 Monomer Library. I believe that the CCP-EM distribution of Coot does the same (although possibly a more recent version). Many ligands have been updated with new restraints from Acedrg, but not ligands with metals. I understand that ligands with metals are being considered - I don't know the current status. It seems unlikely (to me) that the CCP4 Monomer Library will use Phenix restraints. I suppose that it's possible that one could write a script to create a Frankensteinian library where the dictionaries from Phenix replace or fill the gaps in the CCP4 Monomer Library. Seems like a good idea, but not high on my priority list. TLDR: SEP. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
