Hi Laurie, I'm sorry for the trouble! If you provide a heavy_atom file then autosol should not search for additional sites if everything is working ok. In the GUI you should be able to just supply the file and it should be recognized. On the command line you should be able to say sites_file=ha.pdb I just tried that here and it seemed fine. The log file said: HA SITES FILE /net/sigma/raid1/scratch1/terwill/misc/junk/wt056/ha.pdb Reading sites from /net/sigma/raid1/scratch1/terwill/misc/junk/wt056/ha.pdb If that doesn't work for you, can you send me (off-list; [email protected]) the full log file for your autosol run? I'll have a look at it. Now a different question is finding sites closer together than you specify. You can say, hyss_min_distance = 3.5 to only look initially for sites 3.5 A apart with HYSS. However phaser will later try to add sites (if this is a SAD dataset) and they may be closer than that (because they may simply be multiple conformations of a SeMet side chain). I hope that helps! -Tom T All the best, Tom T
If I want to run Autosol with a set of previously determined heavy atom positions (seleno-Met protein) that I might have edited, and NOT search for any more sites, just use those sites for phasing and density modification and model building, I can't seem to find in any of the parameter buttons a way to do this - every time I try it seems to just re-run hyss and find the same sites again.
It seems to find multiple Se sites on top of each other that are closer than the minimum distance I specified in the input.
Thanks
LAurie Betts _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb