Re: [ccp4bb] problems starting pandda.inspect - maybe COOT / CCP4 related

2023-08-08 Thread Paul Emsley 

On 08/08/2023 09:57, Schaefer, Martina wrote:
>
> Hello,
>
>  
>
> I have a problem running pandda.inspect after successful running
> pandda.analyse with the newest ccp4 version of pandda.
>
>  
>
> What do we have:
>
>   * We use Ubuntu as our Linux system
>   * We installed CCP4-8.0.012
>   * When I start pandda.inspect COOT 0.9.8.8.EL opens and the
> following error message appears in the terminal window:
>
>  
>
> INFO:: There are 1 command line scripts to run
>
>    
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> calling run_script() for file
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> debug:: run_script() on
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> Running python script
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
>
> /opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/../resources
>
> No module named matplotlib
>
> Traceback (most recent call last):
>
>   File "", line 1, in 
>
>   File
> "/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py",
> line 1725, in 
>
>     import matplotlib as mpl
>
> *ImportError: No module named matplotlib*
>
> (use-graphics-interface-state)
>
>  
>
> I checked and we do have a matplotlib python module installed (version
> 3.3.4)
>
>  
>
> Has anybody an idea how to tell COOT that the correct matplotlib
> module is present….
>
>  
>

I don't really understand what CCP4 do when packaging Coot.

I can say that I don't like the look of the above though. Coot 0.9.x
uses python 2 (only). Your above error message mentions python3.7 - so
that seems muddled.

It might be that you have a python in the same directory as the coot
executable, so you can (I guess) use that to install matplotllib:

$ which coot

/opt/remote/coot-0.9/bin/coot

so then:

$ /opt/remote/coot-0.9/bin/python -m pip install matplotlib

I suspect that that's not much help.

Paul.





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[ccp4bb] Reg. ITC machine

2023-08-08 Thread Sivaraman Padavattan 
Dear all,

Our department planning to buy Isothermal Calorimetry (ITC). We are in 
discussion with two major players in this segment (MicroCal PEAQ-ITC system 
(Malvern) and Affinity ITC (TA Instruments)). I'd like to ask the ITC users in 
the CCP4 community to give your honest feedback (Pros and Cons) on the above 
machines, which would help us in the decision process.

Greatly appreciate your response. Thank you for your valuable time.

Best,
Sivaraman Padavattan



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[ccp4bb] problems starting pandda.inspect - maybe COOT / CCP4 related

2023-08-08 Thread Schaefer, Martina 
Hello,

I have a problem running pandda.inspect after successful running pandda.analyse 
with the newest ccp4 version of pandda.

What do we have:

  *   We use Ubuntu as our Linux system
  *   We installed CCP4-8.0.012
  *   When I start pandda.inspect COOT 0.9.8.8.EL opens and the following error 
message appears in the terminal window:

INFO:: There are 1 command line scripts to run

/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
calling run_script() for file 
/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
debug:: run_script() on 
/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
Running python script 
/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/../resources
No module named matplotlib
Traceback (most recent call last):
  File "", line 1, in 
  File 
"/opt/remote/ccp4-8.0.012/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py",
 line 1725, in 
import matplotlib as mpl
ImportError: No module named matplotlib
(use-graphics-interface-state)

I checked and we do have a matplotlib python module installed (version 3.3.4)

Has anybody an idea how to tell COOT that the correct matplotlib module is 
present

Thanks, and best regards, Martina


[cid:image001.png@01D9C9E7.2DFF8890]
Martina Schäfer
Principal Scientist
Innovation Campus Berlin
Lead Discovery / Structural Biology
Mobile: +49 173 6652969
Email: martina.schae...@nuvisan.com


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Re: [ccp4bb] PyMol tutorials: Summary

2023-08-08 Thread Aaron Finke 
Hi all,

I’ll add to this list the videos by Pymol Ross- I particularly like his videos 
because he shows how to do things via both the GUI and the command line:

https://www.youtube.com/@pymolross

Best,
Aaron
--
Aaron Finke
Beamline Scientist, MAX IV
Lund University
e-mail: aaron.fi...@maxiv.lu.se

On Aug 4, 2023, at 18:08, Patrick Loll 
mailto:pjl...@gmail.com>> wrote:

Thanks to everyone who responded to my query about PyMol tutorials.  Several 
people evinced interest in seeing a summary of the results, so I’m attaching 
one below:

YouTube tutorials for PyMol:
=

1) Molecular Memory got a number of mentions:

https://www.youtube.com/@MolecularMemory/videos:   e.g. PyMol 101, lessons 1 & 2


2) Another recommended source was the bumbling biochemist site:

https://youtube.com/@thebumblingbiochemist (e.g., 
https://www.youtube.com/watch?v=GpxCGQAhgi8=15s)


3) Keni Vidilaseris has assembled a number of tutorials here:

https://youtube.com/playlist?list=PLfdvnKKZWSxCBL8uDQuc9bAttmAg3-_LS


4) Here are a couple of videos recommended by Mitch Miller:

https://www.youtube.com/watch?v=h5wKppcyzOw  &  
https://guides.lib.vt.edu/c.php?g=947485


5) Here’s a link recommended by Amit Bablekar:

https://www.youtube.com/watch?v=h5wKppcyzOw


6) And for cranky oldsters such as myself, here’s an actual document:

https://dasher.wustl.edu/bio5357/software/pymol/simple-tutorial.pdf


7) Finally, John Hasty also pointed out that there is a Google Colab notebook 
with various PyMol scripts.

Much obliged for the help!

Pat

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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