Hydrogen atoms should always be included in an X-ray model. They are half of the atoms in a protein. They are not refined except in a 'ridding' position, connected to the heavy atom. Molprobity will add hydrogens before any structural analysis and you can't do dynamics or MD without them. Only the orientation of the OH in Tyr, Ser and Thr are in question, but that is the importance of the H bond scheme in any structure. Students should be taught how to add them in any molecular modelling class and to examine the H-bonding. They may even help your R value if the structure is high resolution. Just sayin. kas
Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 ________________________________ From: Mailing list for users of COOT Crystallographic Software <[email protected]> on behalf of Paul Emsley <[email protected]> Sent: Thursday, November 5, 2020 3:41 AM To: [email protected] <[email protected]> Subject: Re: Nature this week They are indeed in the direct map. Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM reconstruction than a map from x-ray data (given the same resolution of the data). "Atomic resolution" of course doesn't refer the the data resolution required to resolve a hydrogen atom and the atom to which it is bonded. On 05/11/2020 09:11, Tim Gruene wrote: > > > Do you know why the hydrogen atoms only show up in the difference map, > but not in the direct map? They are indeed in the direct map. > The signal strength of hydrogens relative to > C, N, O is quite strong, much stronger than for X-rays. Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM reconstruction than a map from x-ray data (given the same resolution of the data). > The large blobs > that you illustrate in the difference map just disappear in the direct > map. Is this expected? After the hydrogens are modelled, they seem to > totally disappear... > This sounds like you've done some refinement of this dataset yourself. Is that what you mean? EMD-11638/7a4m. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT<http://www.jiscmail.ac.uk/COOT>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
