Alan, I guess as industrial crystallographers we are in the same boat. I highly encourage my group to use Hydrogens throughout refinement, not a problem for proteins as phenix.reduce is very good at adding Hydrogens and de novo ligands/inhibitors can be easily defined with Hydrogens as well. I fully agree that "legacy" definitions are a mess in that regard and should be remedied to have hydrogens added. I tend to redefine the cif-files for known ligands to include Hydrogens and use those for internal purposes. Would need to look into the notes from the recent "Ligand Validation Workshop" at Rutgers/PDB if they had taken this into account for future development at the PDB.
Carsten -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[email protected]] On Behalf Of Hruza, Alan Sent: Monday, November 16, 2015 4:48 PM To: [email protected] Subject: Re: [COOT] Heme monomer library entries messed up Oliver, Things get even better when you add hydrogens thru MolProbity onto HEM group and Real Space Refine with coot. Hydrogens blow up! :-( Alan -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[email protected]] On Behalf Of Oliver Clarke Sent: Monday, November 16, 2015 3:42 PM To: [email protected] Subject: Heme monomer library entries messed up Hi all, the geometry of a bunch of heme-related entries in the monomer library is still a bit messed up - see the following screenshots as examples: HEO: https://www.dropbox.com/s/v9cuq5ieqc8xso6/Screenshot%202015-11-16%2015.34.08.png?dl=0 HEB: https://www.dropbox.com/s/fg08ncbul9b3ghi/Screenshot%202015-11-16%2015.33.49.png?dl=0 DHE: https://www.dropbox.com/s/tb0go7yrcwhh1sm/Screenshot%202015-11-16%2015.33.14.png?dl=0 This makes building heme/prophyrin containing structures (which are not so uncommon) a little less convenient than it might be otherwise. Previous report here (https://www.mail-archive.com/[email protected]/msg03388.html). Cheers, Oliver. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
