Hi Tim, Yeah, riding hydrogens have always been on. I guess I need some more investigation.
Chris On Mon, 2012-05-07 at 15:36 +0200, Tim Gruene wrote: > -----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----- -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
