Re: [phenixbb] Problem refining structure, error message

phenix.refine does not use REMARKS. you must have somewhere the selection line. You probably use the automatically generated metal restrains and the atom name there does not match the one in PDB. Can you share your phenix.refine command line? Oleg Borbulevych -----Original Message----- From: "Pavel Afonine" Sent: Thursday, February 18, 2016 8:33pm To: "Natalia Ketaren" , "[email protected]" Subject: Re: [phenixbb] Problem refining structure, error message _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] still remembers about Li.. may be a parameter file from previous run or something else... I'm actually curious to know what is that, so please post your solution once you have it. Is it really remark records?.. Pavel On 2/18/16 17:00, Natalia Ketaren 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 [email protected] mailto:[email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]