[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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