The dynamo2m from alisterburt

dynamo2m's Introduction

🙃 Alister Burt                                                                                     
┣━━ 🔬 Research Interests                                                                           
┃   ┣━━ cryo-electron tomography - enabling in situ protein structure determination                 
┃   ┗━━ bacterial chemotaxis - how bacteria sense and respond to nutrients/toxins                   
┣━━ 📦 Open Source Packages                                                                         
┃   ┣━━ napari - n-dimensional data visualisation in Python                                         
┃   ┣━━ blik - browse cryo-ET data and annotations in napari                                        
┃   ┣━━ napari-animation - make animations in napari                                                
┃   ┣━━ dynamo2m - combine dynamo and warp/relion/m                                                 
┃   ┣━━ eulerangles - fast conversion of large sets of Euler angles                                 
┃   ┗━━ starfile - STAR file IO in Python                                                           
┣━━ ⭐ Web Projects                                                                              
┃   ┗━━ teamtomo.org   - cryo-ET knowledge platform                                                 
┣━━ 🎙️ Teaching                                                                                      
┃   ┣━━ EMBO image processing for cryo electron microscopy                                          
┃   ┣━━ EMBO advanced methods in bioimage analysis                                                  
┃   ┣━━ EMBO cryo-electron microscopy and 3D image processing                                       
┃   ┣━━ Dynamo workshop - Basel, CH                                                                 
┃   ┣━━ Intro to bioinformatics - Université Grenoble Alpes                                         
┃   ┗━━ Multidisciplinary experimental methods - Université Grenoble Alpes                          
┗━━ 👨‍💻 Employer                                                                                   
    ┣━━ MRC-LMB - Postdoc in David Barford's group                                                  
    ┗━━ ⏰ Previously...                                                                            
        ┣━━ CCP-EM - collaborative computational project for electron microscopy                    
        ┗━━ Institut de Biologie Structurale - PhD student in Irina Gutsche's group
        ┣━━ Diamond Light Source - Intern on B24                                                    
        ┗━━ CHyM - Intern                           

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dynamo2m's Issues

Script compatibility with Dynamo catalogue

Hi, I have 200 tomograms and the corresponding models in a Dynamo catalogue. How do I produce a STAR file for multiple tomograms in a catalogue? I A Doc file is needed for the scipt - how should this be created? Many thanks for any tips.

Problem with one-particle star file

Hi Alister,

I have a problem running the warp2dynamo script and it seems to only happen when the star file only have one particle.

Traceback (most recent call last):
  File "/home/janlevinson/micromamba/envs/dynamo/bin/warp2dynamo", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/dynamo2m/warp2dynamo.py", line 108, in cli
    warp2dynamo(warp_star_file, dynamo_table_file, extracted_box_size)
  File "/home/janlevinson/micromamba/envs/dynamo/lib/python3.12/site-packages/dynamo2m/warp2dynamo.py", line 38, in warp2dynamo
    dynamo_data['tdrot'] = eulers_dynamo[:, 0]
                           ~~~~~~~~~~~~~^^^^^^
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

The error goes away after adding a dummy line.

I know this is a very rare case. But we do often work on very rare targets.

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