[phenixbb] phenix.refine does not work with afitt
guenter.fritz.phenix.ccp4 at gmail.com
Sun Dec 30 02:25:34 PST 2018
some days off do wonders :).
I made a mistake and had a conflict in setting the variables. I had in
but in the .openeyerc.bash I had it again but with an additional "e" in
This messed things up.
Thanks a lot and already now Happy New Year!
> 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.
> 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
> 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?
>> 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
>> 188.8.131.52). 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
>> Any help is appreciated. Thanks and best regards,
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> Unsubscribe: phenixbb-leave at phenix-online.org
>> <mailto:phenixbb-leave at phenix-online.org>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb