[phenixbb] refine error message

Engin Özkan eozkan at uchicago.edu
Mon Sep 18 09:02:53 PDT 2017

Hi Jiemin,

I recently had a few errors of such, and while I can't remember which 
Phenix program spitted it out (Phaser or phenix.refine), the issue was 
my models from MODELLER. Simply deleting hydrogens by running

phenix.reduce -Trim insertpdbname.pdb >newpdbname.pdb

on the coordinate file fixes it for me.

I might be way off with your issue, but this is easy enough to try.


On 9/18/17 10:57 AM, Jiemin Zhao wrote:
> Hi,
> I got an error message when I try to refine a molecular replacement 
> result. It says Fatal problems interpreting model file: Number of 
> atoms with unknown nonbonding energy type symbols: 18 Please edit the 
> model file to resolve the problems and/or supply a CIF file with 
> matching restraint definitions, along with apply-cif-modification and 
> apply-cif-link parameter definitions if necessary.
> Could you help me with this problem?
> Thanks!
> Best regards,
> Jiemin
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