Dear Janine, I’ve just tested this on some of our own data, and indeed it looks like this command-line script has been inadvertently broken. We’re probably not using it a lot ourselves, which is why we didn’t notice, so we should probably implement a routine test! In the meantime, there are a couple of other approaches you could use. The closest to this script would be to run the Phaser-EP Phenix GUI, choose the MR-SAD phasing mode, provide your model coordinates as “Partial model”, and then enter “AX” for the scattering type you’re looking for; AX is the name used for a purely imaginary scatterer, which is the most sensitive way of identifying anomalous scatterers in a well-refined structure. It’s also possible to do something similar in the AutoSol GUI, or from the command line by passing the right options to phenix.autosol. Let me know if you need any help, and we’ll try to get this script fixed! Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

On 23 Mar 2018, at 16:17, Janine Gray wrote:

Hi,

I am trying to run phaser.find_anomalous_substructure to identify the anomalous peaks of some phosphorus atoms and get the following error:

AttributeError: 'NoneType' object has no attribute 'as_pdb_string'

Looking in the log file), it states a file opening error with my PDB file:

****************************************************************************************** *** Phaser Module: AUTOMATED EXPERIMENTAL PHASING 2.8.1 *** ******************************************************************************************

** Steps: ** Anisotropy correction ** Experimental Phasing ** SAD Phasing

CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs) Finished: Fri Mar 23 15:23:15 2018

****************************************************************************************** *** Phaser Module: SINGLE-WAVELENGTH ANOMALOUS DISPERSION 2.8.1 *** ******************************************************************************************

Keyword input too long to echo to output (>10000 characters)

------------------------------------------------------------------------------------------ FILE OPENING ERROR: ATOM 1 N MET A 1 5.825 -12.222 -3.663 1.00 89.47 N

Has anyone seen this before and/or knows how to fix this?

Cheers,

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