Hi Michael,
I recently installed panDDAs on an older Linux system. It still runs Centos
7, which was nice since I've run into compatibility issues with
python3/python 2.7 on a newer Mac.
Here are the basic steps that I've had to follow:
--Install cpp4 7.0 and download the updates to get to the right version
(7.0.72)
--source the correct ccp4
--Installed panddas according to the instructions found on the panddas page
--*I installed an older version of Pymol that still used python 2.7, not
sure if this is 100% necessary, but I did it to try to make sure no more
python errors would happen
--In the classes.py script, change c=CommandManager('source of pymol') to
where my pymol was installed (my Linux box has a weird hard drive system)
Then panddas ran correctly! Hopefully the new version on Friday fix your
issues, but if they don't, feel free to let me know, and I can try to help
you troubleshoot more.
Thanks,
Jessica
On Tue, Feb 14, 2023 at 2:17 AM Michael Weyand <
[email protected]> wrote:
> Dear colleagues,
>
> First, I don't want to flood ccp4bb with all the concrete program error
> code(s). Therefore a more general description. I can give more details if
> needed. To the board or by direct mails to the real experts.
>
> I would like to use the Panndda/PanDEMIC
> <https://pandda.bitbucket.io/index.html#> tools within our CCP4
> environment (version 8.0.008) but I ran in some Python issues, although
> CCP4 patch 8.0.005 claimed various py3 Python fixes for Pandda. Even more
> by using the 2to3 <https://docs.python.org/3/library/2to3.html> Python
> version converter I found a number of Python3 (syntax and more) issues in
> the *main* CCP4 Python3 folder/subfolders at
> /ccp4/ccp4-8.0/lib/python3.7/site-packages/
>
> Since my OS (openSuSE Leap 15.4) still comes with both Python version 2.7
> and 3.6 and CCP4 now comes (to my knowledge) with 3.7 I am confused what I
> have to correct/change to use the Pandda tools. By my error tracking I'm
> pretty sure that PATH and PYTHONPATH are directing to the CCP4 folders, but
> may be I'm wrong ...
>
> And/or what was changed to the Pandda tools in the 8.0.005 CCP4 patch?
> Obviously, they are not working at my site ... :-(
> For instance, all Pandda scripts are still coming with a Python3 obsolete
> program option "-Q" ?!?!
> Was my 8.0.005 patch not properly executed? CCP4i teils me nothing.
>
> It is a shame but my Python knowledge is more than limited. Therefore I
> ran 2to3 for all Pandda scripts but then main CCP4 Python tools/scripts
> showed up, again with some syntax errors (= missing version 2/3 conversion
> ??) in the code. After also correcting these first 2-3 issues there were -
> by executing "pandemic.adp" - still more and more Python issues
> appearing...
>
> Now I asked my self, what is wrong with my CCP4 installation? According to
> patch 8.0.005 these tools should run !!
>
> And why are there version 3 issues beyond the CCP4 python3.7 folder ??
> I'm confused. Any help is highly appreciated.
>
> Best,
> Michael
>
>
>
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