[phenixbb] Problem refining structure, error message

Singh, Bishal b.singh at dkfz-heidelberg.de
Thu Feb 18 17:24:51 PST 2016

Hi Nat,
Open your PDB file in text, remove information of Li in 'remark', save the  pdb file and use it for refinement. This should work.

Bishal Singh, PhD student
German Cancer Research Center (DKFZ)
University of Heidelberg

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Natalia Ketaren [nketaren at mail.rockefeller.edu]
Sent: Friday, February 19, 2016 2:00 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Problem refining structure, error message


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?



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<mailto:Natalia.Ketaren at rockefeller.edu>
website: http://lab.rockefeller.edu/rout/
NCDIR: http://www.ncdir.org/

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