To also generate source maps for the JupyterLab core extensions, you can run the following command: jupyter lab build -minimize =Falseĭevelopment uninstall pip uninstall jupyterlab-unfold Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).īy default, the jlpm run build command generates the source maps for this extension to make it easier to debug using the browser dev tools. With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. # Watch the source directory in one terminal, automatically rebuilding when needed You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension. # Rebuild extension Typescript source after making changes # Link your development version of the extension with JupyterLab
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# Clone the repo to your local environment # Change directory to the jupyterlab-unfold directory # Install package in development mode The jlpm command is JupyterLab's pinned version of Note: You will need NodeJS to build the extension package. To remove the extension, execute: pip uninstall jupyterlab-unfold Result of angles = as above.To install the extension, execute: pip install jupyterlab-unfold I think the key to the molecule being linear however, is that the 2 angles must cancel out. Update, a slight improvement in SS can be obtained with using the angles 90 and -90, though there is still some rotation along the total length of the sequence, so the 'correct' angle for a perfectly linear molecule is likely slightly lower. Here's the secondary structure colour coded for clarity: It seems the angles are not as simple as (0, 0)įor r1, r2 in zip(m.residues, n.residues):Ĭlose! - but needs more tinkering as I said. We can then try copying over the secondary structure attributes, but this isn't perfect at the moment. Which will add another model to the view: Maybe it helps?Ĭan't take credit for this, was all Jaime's input, I just consolidated it.įrom inside chimera (or using P圜himera): import chimeraĪngles = There might be other options to explore in the peptideBuilder though. The angles are also not quite right, so the secondary structure is a bit off. Here's an approach, but far from perfect, though does produce a perfectly linear model (but can be quite slow).
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Still, I am not sure how to adjust the angles propperly Output looks good (red helix, green strand), now the angles.? Make_pdb_file(build_linear_model_from_sequence(myseq), outfile)Īdded secondary structure annotation from the original PDB structure by copy-paste. Model_structure=PeptideBuilder.add_residue(model_structure, model_structure_geo) Model_structure=PeptideBuilder.initialize_res(model_structure_geo)įor i in range(1,len(model_structure_geo)): My 'first python script': from _future_ import print_functionĭef build_linear_model_from_sequence(seq): Now, modifying def build_linear_model(pdb_filename): looks promising. There doesn't seem to be a Vector module but Vector is a type imported already ?.Īfter commenting out from import * and changing print i to print (i), the script produces some output. So, in PeptideBuilder.py, comment out: from import * Type "help", "copyright", "credits" or "license" for more information.įile "/Users/mdondrup/miniconda/envs/py2/lib/python2.7/site-packages/PeptideBuilder/_init_.py", line 10, in įile "/Users/mdondrup/miniconda/envs/py2/lib/python2.7/site-packages/PeptideBuilder/PeptideBuilder.py", line 22, in Try to load the package: Python 2.7.15 | packaged by conda-forge | (default, Jul 2 2019, 00:42:22) I assume it's Python 2.7: conda create -name py2 python=2.7 Ok, so here is my first update, I installed Peptide builder and it works(?). As you can see, the linear model is far from perfect.
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Here is a little movie trying to explain what I want to achieve. I also have the i-Tasser output, if that helps. I tried to quickly flatten the structure manually, but that is not really convenient. Please let me know if the description of the task is unclear.īackground: I wish to create a little protein movie in Chimera using its morph tool, where the 2D cartoon structure morphs into the 3D ribbon structure. Is there possibly an easy way to do that? The output would preferentially be in PDB format again.
So this might be called reversing the 3D-folding of the structure. Of course,Ĭontained helices and sheets should still be rendered correctly. Linearized form representing only the secondary structure, as a long flat chain of secondary structures from C to N terminus along the linear backbone. I would like to transform the 3D model into a I have a protein structure (generated by i-Tasser) in PDB format. I need a quick hack for the following problem:
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