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