Is there a chance that ThDP (TDP or TPP in the ccp4 dictionary) is restrained differently in 6.1.x than it used to be in 6.02 or even earlier versions (e.g. 5.2) ?
Boaz ----- Original Message ----- From: Eleanor Dodson <c...@ysbl.york.ac.uk> Date: Thursday, March 19, 2009 11:17 Subject: Re: [ccp4bb] nad woes To: CCP4BB@JISCMAIL.AC.UK > Even for NAD I think I would make my own "new" dictionary. > > If you go to the ebi site ( now pdbe) ask for Msdchem ( is it > PDBeChem > now?) > Get the idealised NAD coordinates with the remediated nomenclature > Submit the coordnates to the ProDrg server. > Retrieve the REFMAC dictionary > > Use PDB and dictionary in Coot to fit the ligand.. > > Eleanor > > > > Get back an idealised dictionary Jan Abendroth wrote: > > Hi all, > > is there any wisdom on NAD out there? I experience some > strange > > behaviour of this common cofactor. > > > > With moderately convincing density, probably low occupancy of > a > > cofactor that came along for the ride from E coli, > Refmac5.5.0088 > > pulls the AN6 atom out of the adenine plane. With my own > library that > > puts planar restraints on the adenine ring this seems to be fixed. > > > > Coot during real space refinement or regularisation using > either the > > standard or my own dictionary handles the purine ring just > fine, > > however, totally garbles up the nicotineamide. > > > > Btw, I use the * nomenclature. > > > > Cheers > > Jan > > > > -- > > Jan Abendroth > > deCODE biostructures > > Seattle / Bainbridge Island WA, USA > > work: JAbendroth_at_decode.is > > home: Jan.Abendroth_at_gmail.com > > > > > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
