[phenixbb] phenix.refine does not work with afitt

Guenter Fritz guenter.fritz.phenix.ccp4 at gmail.com
Tue Dec 25 15:13:05 PST 2018

Hi Nigel,

yes, I did follow the instructions and afitt is running. Path is set. It 
should be properly installed.
The afitt gui works to write inputs for refmac and calls also refmac. 
The afitt gui prepares also the input files for phenix but phenix.refine 
fails then with the error below.

"Sorry: Unknown command line parameter definition: use_afitt = True"

Same in the command line or if I try afitt.run_tests. It looks as if 
phenix does not recognize the keyword use_afitt=True.

PS: There must be also a typo on the instructions page:
The example on the page for the command is :

phenix.refine mymodel.pdb mymodel.mtz myligand.cif use_afitt=True
        afitt.ligand_file=myligand.cif afitt.ligand_names=UNL,BCL

Below in the list of required keywords it is


Anyhow this is not the cause for the error.

I guess I overlook some detail.  I will test some older versions and the 
latest builds.

I wish you have some relaxing days! Season Greetings and best wishes, 

PPS there is absolutely no hurry for this,cheers

> AFITT is still supported and tested nightly.
> Did you follow the instructions here?
> https://www.phenix-online.org/documentation/reference/afitt.html
> Cheers
> Nigel
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://CCI.LBL.gov>
> On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz 
> <guenter.fritz.phenix.ccp4 at gmail.com 
> <mailto:guenter.fritz.phenix.ccp4 at gmail.com>> wrote:
>     Dear phenix developers,
>     I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt
> However, I receive the an error:
>     "Sorry: Unknown command line parameter definition: use_afitt = True"
>     This I get on my mac or on my linux box. Is support for afitt
>     discontinued?
>     Any help is appreciated. Thanks and best regards,
>     Guenter
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