Jim wrote: "technically, not in Phenix either. The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them. . Like a black hole gobbling up nearby planets (snip)" Do you have a reference to support this assertion? "It took me a while to realize that! If you manage to turn off geometry restraints (as I eventually did) all the atoms end up on top of each other." As expected if no bond distance is enforced, unless you have very high resolution to the point that density for each atom becomes discrete. Since that is very unlikely to be your case your observation: does not prove anything about how Phenix works. >From phenix.refine documentation:
"Coordinates can be refined using: * (snip) * individual coordinate refinement in real-space using a combination of gradient-driven (LBFGS) minimization and local torsion-angle grid searches" Hopefully someone from the Phenix team will give some clarifications. But the statement above indicates that Phenix is capable of performing real space refinement by some other means than the "black hole approach". Thierry 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. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
