Hi Kaibo,

I'm sorry about that!  You're right...autosol does not pass place_waters=False correctly to phase_and_build and so refinement includes waters even if you set it to False.  I have fixed this now and starting with tomorrow's nightly build it should work properly. Let me know if that doesn't do it!

In most circumstances adding waters in early stages of refinement is just a way to say "there is something here" rather than "this is a water" and so it should normally be fine to leave it as place_waters=True. 

All the best,
Tom T


On Wed, Mar 7, 2018 at 12:53 PM, Kaibo Zhang <zhang644@purdue.edu> wrote:
Helllo,
I was using AutoSol GUI for MR-SAD of my data and trying to  turn off "place waters in refinement". However, the output pdb files still got waters in them. I did check the run log file and confirmed both the "place_waters" and the "flood_with_waters" flags were set to false. But in the later session, it still recorded "adding waters in refinement". 

Is there any parameters I should adjust to avoid adding waters during the Autosol run. Or is it just turned on in the end in order to calculate R_work/free, and doesn't affect your phasing solution?

Look forward to your responses. Thank you in advance!

 Regards
Kaibo 

Kaibo
PULSe, Purdue University
Hockmeyer Hall, Room 321
240 S. Martin Jischke Drive, West Lafayette, IN 47907

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org



--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Tel: 505-431-0033