[phenixbb] Problem refining structure, error message

oleg at quantumbioinc.com oleg at quantumbioinc.com
Thu Feb 18 18:07:15 PST 2016


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" <pafonine at lbl.gov>
Sent: Thursday, February 18, 2016 8:33pm
To: "Natalia Ketaren" <nketaren at mail.rockefeller.edu>, "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Problem refining structure, error message

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Unsubscribe: phenixbb-leave at phenix-online.orgSomething 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
> 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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