Hi Paul,
Thanks for this. Unfortunately its BIOMT records that I have, not MTRIX records. I don't suppose you have a corresponding "biomt-to-refmac-ncs-matrix.awk script"?
Out of interest I tried this on a PDB file that does have MTRIX records but it bailed out at source line 1. My awk skills are non-existent, so I couldn't fix it...
Thanks again
Dave
-------------------------------
Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [log in to unmask]
-----Original Message-----
From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> On Behalf Of Paul Emsley
Sent: 09 April 2019 14:58
To: [log in to unmask]
Subject: Re: [ccpem] icosahedral virus issues
On 09/04/2019 14:06, david lawson (JIC) wrote:
>
> Yes the phenix.pdb.biomt_reconstruction PDB file does contain non-standard two-character chain IDs.
>
> phenix.pdb_as_cif processes this PDB without any problems (as far as I
> can tell)
>
> I don’t suppose you (or anyone else for that matter) has a handy
> script to convert the BIOMT records into
> REFMAC5 "ncsconstraints" keywords? Alternatively the refmac
> documentation indicates that it will read MTRIX records in the pdb
> header if no ncs operators are given. So a quick way to convert BIOMT
> records to MTRIX records would be nice 😉
I'm not sure that I follow the need for tight NCS restraints, but here's the mtrix converter.
$ awk -f mtrix-to-refmac-ncs-matrix.awk pdb > ref.key
Paul.
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