[phenixbb] Problem refining structure, error message

Billy Poon bkpoon at lbl.gov
Thu Feb 18 17:27:44 PST 2016

Hi Natalia,

Are you using old settings to refine your new structure? If you're using
the GUI, try starting with a new job (e.g. clicking on phenix.refine
instead of restoring an old job). If you're using the CLI, you can send me
your parameter file (ends with .eff) and I can take a look. There could be
a selection for Li that is floating around if you're using the same
parameter file from and earlier job.

Let me know if that doesn't work for you. Thanks!

Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Thu, Feb 18, 2016 at 5:00 PM, Natalia Ketaren <
nketaren at mail.rockefeller.edu> wrote:

> Hello,
> I’m building a structure at the moment, and I have since removed lithium
> ions from structure. However, when I go to refine using phenix, I get the
> error message:
> “No atom selected: name LI and Chain F and rename LI resseq 8”
> I’ve tried using earlier files, prior to my addition of lithium ions and I
> still get the same error message. I’m using Phenix version 1.10.1-2155-000
> Could anyone help me overcome this error message?
> Cheers,
> Nat
> _____________________________
> Natalia E. Ketaren, PhD
> Research Associate
> Rout Laboratory
> Box 213
> The Rockefeller University
> 1230 York Avenue
> New York, NY 10065
> Tel: (212) 327-8136
> Fax: (212) 327-7193
> Natalia.Ketaren at rockefeller.edu
> website: http://lab.rockefeller.edu/rout/
> NCDIR: http://www.ncdir.org/
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