Dear Nat,

You are right.

I added two metal ions Zn and Mg and after that I started getting this error.

I did run phenix.metal_coordination to get elbow.edits and add this to refinement to to get same error.

I am not running with water update option.

I ran the pdb through readyset and added metal restraints, processed pdb file and ligand restraints to the refinement to get same error.

The Zinc and Mg are not coordinated well. I have added because nothing fits in the density. I am not sure lack coordination is creating the problem. I will send ATOM records to Pavel.

Thanks a lot for looking in to this one.

SDY

From: [email protected]
Date: Tue, 4 Mar 2014 07:50:31 -0800
Subject: Re: [phenixbb] phenix error
To: [email protected]
CC: [email protected]

You probably have metal coordination restraints that are no longer valid - each time you run phenix.refine with the solvent update enabled, the numbering of waters will change and the old restraints become invalid. �The utilities menu in the phenix.refine GUI has an option to clear these out entirely; you can then run ReadySet again to generate new restraints.

-Nat

On Mon, Mar 3, 2014 at 10:31 PM, SD Y <[email protected]> wrote:

Hi,

Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69".�

Log file ends as follows:

============================= Scattering factors =============================

� � � � � � � � ----------X-ray scattering dictionary---------- � � � � � � � �

Number of scattering types: 7
� Type �Number � �sf(0) � Gaussians
� �Zn2+ � � 1 � � 27.88 � � � 1
� �S � � � 10 � � 15.96 � � � 2
� �P � � � �2 � � 14.95 � � � 2

� �Mg2+ � � 3 � � �9.96 � � � 1
� �O � � �635 � � �7.97 � � � 2
� �N � � �523 � � �6.97 � � � 2
� �C � � 1983 � � �5.97 � � � 2
� sf(0) = scattering factor at diffraction angle 0.

========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

======================== Summary of geometry restraints =======================

� Number of disulfides: simple=0, symmetry=0
� Custom bonds:
Sorry
------------------------------

Thanks a lot
SDY

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