[phenixbb] phenix.refine does not work with afitt

[Nigel Moriarty]

Glad to hear it!

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 Sun, Dec 30, 2018 at 2:25 AM Guenter Fritz <
guenter.fritz.phenix.ccp4 at gmail.com> wrote:

> Hi Nigel,
>
> some days off do wonders :).
> I made a mistake and had a  conflict in setting the variables. I had in my
> .bash_profile
> export OE_EXE='/usr/local/bin/flynn'
>
> but in the .openeyerc.bash I had it again but with an additional "e" in
> "usr"
> export OE_EXE='/user/local/bin/flynn'
>
> This messed things up.
>
> Thanks a lot and already now Happy New Year!
> Guenter
>
> 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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
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>>>
>>
>>
>
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