-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Chris,
If the absence/ presence of hydrogens in the coordinate file made a difference in the refinement, I guess some parameter setting for the refinement program is awkward. Did you refine with riding hydrogens in both cases? Hydrogens can and should be added in riding positions even at low resolution, since they do not add to the number of parameters but help with anti-bumping restraints. Tim On 05/07/12 15:07, Christopher Browning wrote: > Hi, > > I've generally used PRODRG to create paramater files for any > ligands I add during refinement with CCP4 and/or PHENIX. I've been > trying READYSET from PHENIX as it greatly helps refining some metal > ion positions. But when I use READYSET, any ligand I add (in this > case EDO or ethylene glycol) gets modified to contain hydrogens. My > resolution is 2.5, definitely not high enough to resolve the > hydrogens, so why are they added. Should I just leave them there? I > have the same problem with another structure which has bizarre > sugar molecules so they are not standard COOT/CCP4/PHENIX small > molecules. > > As a test, I removed the hydrogens added to the ligands and the > refined protein coordinates are way different than when the > hydrogens are left in? > > > Cheers, > > Chris > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPp8/jUxlJ7aRr7hoRAl2PAJ0WG7405GO1V96UzzFJd53x7rijwQCfeA1i NOGF4DTnAQNGxe6N4mbpXLM= =ov1h -----END PGP SIGNATURE-----
