Re: [ccp4bb] Hydrogens added when using Phenix Readyset for ligands

2012-05-07 Thread Pavel Afonine
Hi Chris, - there is Phenix mailing list for Phenix-related questions. Please check http://www.phenix-online.org/ - the data resolution of 2.5A does not mean hydrogen atoms are not present in the crystal. There are methods to account for them. For details see (and references therein): "On contri

Re: [ccp4bb] Hydrogens added when using Phenix Readyset for ligands

2012-05-07 Thread Christopher Browning
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 > dif

Re: [ccp4bb] Hydrogens added when using Phenix Readyset for ligands

2012-05-07 Thread Tim Gruene
-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 sh

[ccp4bb] Hydrogens added when using Phenix Readyset for ligands

2012-05-07 Thread Christopher Browning
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) get