[phenixbb] Questions about the Autosol water placing option

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Wed Mar 7 12:53:06 PST 2018

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 at 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
> Telephone: 765-337-1955 <(765)%20337-1955>
> E-mail: zhang644 at purdue.edu
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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