[phenixbb] phenix.refine does not work with afitt

[Nigel Moriarty]

What is the value of  $OE_EXE?

BTW. I don't think it's a typo as PHIL will match a keyword if the search
finds a unique match which I believe is the case this time.

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


On Tue, Dec 25, 2018 at 3:13 PM Guenter Fritz <
guenter.fritz.phenix.ccp4 at gmail.com> wrote:

> 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
>
> "afitt.ligand_file_name"
>
> 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,
> Guenter
>
> 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
>
>
> On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz <
> 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
>> 2.4.1.2). 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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>>
>
>
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