Dear Kay, Indeed, some programs may come and go over time, becoming obsolete or replaced by others. Also, some command line programs are experimental and can disappear if we find that wasn't a good idea. I don't remember off the top of my head exactly what happened to mmtbx.water_screen, but my guess is that doing anything with waters isn’t too useful without involving refinement. This is because water oxygen is the hardest item to model reliably, simply because water density peaks and noise peaks are very similar. For example, the side chain of tyrosine has a very distinct shape that is hard to confuse with anything else, while water presents just an approximately spherical peak. Your only guide to differentiate it from noise is the presence of plausible hydrogen bonds. However, who’s to say that a noise peak can’t arise in a location that is within plausible hydrogen-bond distances from neighbors? Anyways, phenix.refine has had the option to add, remove, or refine water for years, and that’s the best you can get out of automated (blind, user-involvement-free) water placement in Phenix. Keep in mind what I just wrote: it won’t be error-free, so manual checks are always warranted! It also has the option to place elemental ions, as described here: https://journals.iucr.org/d/issues/2014/04/00/lv5059/index.html Let me know if this does not fit your goals, and we can brainstorm a solution! All the best, Pavel On 1/15/26 02:52, Kay Diederichs wrote:
Dear developers,
CCP4wiki (https://wiki.uni-konstanz.de/ccp4/index.php/Properties_of_proteins) mentions mmtbx.water_screen as a program that can tell ions from water, given a PDB file. Tried that with a recent Phenix installation but the program no longer exists. Is there any similar functionality available?
Thanks, Kay _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s