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<div class="moz-cite-prefix"> Nigel,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thanks a lot. Overall, if Ubuntu is not
ready yet, then I will simply use a Centos box, no problem.<br>
</div>
<div class="moz-cite-prefix">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 <br>
</div>
<div class="moz-cite-prefix">
<div class="moz-cite-prefix"><i><br>
</i></div>
<div class="moz-cite-prefix"><i>$ phenix.refine 4phenix_1a0b.pdb
use_amber=True \ </i><i><br>
</i><i>> amber.topology_file_name=4amber_1a0b.prmtop \ </i><i><br>
</i><i>> amber.coordinate_file_name=4amber_1a0b.rst7 \ </i><i><br>
</i><i>> amber.order_file_name=4amber_1a0b.order \ </i><i><br>
</i><i>> 1a0b.mtz </i><i><br>
</i> <i><br>
</i><i>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) </i><i><br>
</i><i>#phil __OFF__ </i><i><br>
</i> <i>..... </i><i><br>
</i><i>Processing inputs. This may take a minute or two. </i><i><br>
</i><i>Sorry: Unknown command line parameter definition:
use_amber = True</i></div>
<div class="moz-cite-prefix"><i><br>
</i></div>
<div class="moz-cite-prefix"><i>Best regards,</i></div>
<div class="moz-cite-prefix"><i>Guenter<br>
</i></div>
<div class="moz-cite-prefix"><i><br>
</i></div>
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cite="mid:CANkP=2dcTRg60uOSPC426bAmmMb0w+GJotxNs1d1ShdRQm6vmg@mail.gmail.com">
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<div dir="ltr">
<div dir="ltr">Guenter</div>
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<div>
<p>I cannot get the Amber and AFITT menu bars in the
phenix.refine GUI on a Ubuntu (Xubuntu 18.04) box. <br>
</p>
</div>
</blockquote>
<div>Do you have AFITT installed and setup following <a
href="https://www.phenix-online.org/documentation/reference/afitt.html"
moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/afitt.html</a></div>
<div><br>
</div>
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</blockquote>
I have overlooked that. I usually install it an all machines, but
forget this one.<br>
<blockquote type="cite"
cite="mid:CANkP=2dcTRg60uOSPC426bAmmMb0w+GJotxNs1d1ShdRQm6vmg@mail.gmail.com">
<div dir="ltr">
<div class="gmail_quote">
<div>Regarding Amber, Ubuntu is the problem child for many
things including Phenix-Amber. I'm hoping Billy can help
here.</div>
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<p> </p>
<p> I set Preferences "Enable alpha-test programs and
features" (works on my Mac 10.14.6 and SciLinux6 box ).<br>
</p>
</div>
</blockquote>
<div>Don't think this matters for Amber anymore as it's
distributed with Phenix. </div>
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<p> </p>
<p><br>
</p>
<p>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:</p>
<p><i><i>$ phenix</i></i></p>
<p><i>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 <br>
</i></p>
</div>
</blockquote>
<div>Does it crash? Billy probably has the answers here.</div>
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<div>
<p><i> </i></p>
<p><br>
<i><i>------------------------</i></i></p>
<p>python 3.7 is installed and python development tools :<i><br>
</i></p>
<p><i>------------------------<br>
</i></p>
<p><i>$ python -V </i><i><br>
</i><i>Python 3.7.6 </i></p>
<p><i>$ sudo apt list -a python3.7-dev </i><i><br>
</i><i>Listing... Done </i><i><br>
</i><i>python3.7-dev/bionic-updates,now 3.7.5-2~18.04
amd64 [installed] </i><i><br>
</i><i>python3.7-dev/bionic-security 3.7.3-2~18.04.1
amd64 </i><i><br>
</i><i>python3.7-dev/bionic 3.7.0~b3-1 amd64 <br>
</i></p>
<p><i>------------------------</i></p>
</div>
</blockquote>
<div>Phenix 1.18.2 should be the last major release to use
Python2 so you need to have it available.</div>
</div>
</div>
</blockquote>
<br>
<blockquote type="cite"
cite="mid:CANkP=2dcTRg60uOSPC426bAmmMb0w+GJotxNs1d1ShdRQm6vmg@mail.gmail.com">
<div dir="ltr">
<div class="gmail_quote">
<div>Nigel <br>
</div>
</div>
</div>
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