[phenixbb] phenix.refine does not work with afitt

Guenter Fritz guenter.fritz.phenix.ccp4 at gmail.com
Sun Dec 30 02:25:34 PST 2018


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 <http://CCI.LBL.gov>
>
>
> On Tue, Dec 25, 2018 at 3:13 PM Guenter Fritz 
> <guenter.fritz.phenix.ccp4 at gmail.com 
> <mailto: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
>>     <mailto: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
>>         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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