Nigel,

thanks a lot. Overall, if Ubuntu is not ready yet, then I will simply use a Centos box, no problem.
Just a note: I checked also another Ubuntu box to rule out individual problems. The refinement crashes, here, e.g. I used the example of your webinar

$ phenix.refine 4phenix_1a0b.pdb use_amber=True \
>     amber.topology_file_name=4amber_1a0b.prmtop \
>     amber.coordinate_file_name=4amber_1a0b.rst7 \
>     amber.order_file_name=4amber_1a0b.order \
> 1a0b.mtz

Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh# Date 2020-06-04 Time 11:26:08 CEST +0200 (1591262768.33 s)
#phil __OFF__
.....
Processing inputs. This may take a minute or two.
Sorry: Unknown command line parameter definition: use_amber = True

Best regards,
Guenter

Guenter

I cannot get the Amber and AFITT menu bars in the phenix.refine GUI on a  Ubuntu (Xubuntu 18.04) box. 

Do you have AFITT installed and setup following https://www.phenix-online.org/documentation/reference/afitt.html

I  have overlooked that. I usually install it an all machines, but forget this one.
Regarding Amber,  Ubuntu is the problem child for many things including Phenix-Amber. I'm hoping Billy can help here.

 I set Preferences "Enable alpha-test programs and features"  (works on my Mac 10.14.6 and SciLinux6 box ).

Don't think this matters for Amber anymore as it's distributed with Phenix. 


Moreover, on the Xubuntu machine: when I start the phenix.refine GUI (phenix version 1.18.2-3874) I see the following error message in the terminal running phenix:

$ phenix

Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh

Does it crash? Billy probably has the answers here.


------------------------

python 3.7 is installed and python development tools :

------------------------

$ python -V
Python 3.7.6

$ sudo apt list -a   python3.7-dev
Listing... Done
python3.7-dev/bionic-updates,now 3.7.5-2~18.04 amd64 [installed]
python3.7-dev/bionic-security 3.7.3-2~18.04.1 amd64
python3.7-dev/bionic 3.7.0~b3-1 amd64

------------------------

Phenix 1.18.2 should be the last major release to use Python2 so you need to have it available.

Nigel