Hi Brad, The HB_score detects hydrogen bonds and inter-atomic clashes between ligand and protein. This additional term usually helps differentiate best one among a few good fits. If you use the default library, since it consists of a diverse set of candidate ligands, the outcome of fitting the same density could be very different. It is not unusual to see wide spread HB_scores. In the final ranking, we use normalized HB_scores as one of the criteria. Hope this helps. I'll add these information to PHENIX documentation. Please feel free to ask me additional question related to ligand_identification on/off Phenix list. Li-Wei Hung Brad C. Bennett wrote:
Hello to all- Where can I find a description of what "HB_score" is and how it is calculated in the Ligand Identification program in Phenix? I'm assuming this is a metric for hydrogen bonding capability/propensity of a fit ligand based on distance and angle to model atoms. I have an output rank list of the top 20 ligand fits, ranked by Z-score. The HB_score is all over the place: low = -0.59, high = 77.96, most are between 0-10. I think I understand the correlation coefficient and Z-score but how does the HB_score fit in with these?
I can't find this in the documentation or in the Terwilliger et al. (2007) Acta D reference. Somehow I've "lost" the log file, so maybe the information is in there.
Thanks in advance!
Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: [email protected] Lab phone: 434-243-2520 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb