User:Wayne Decatur/Code for Molecular Structure and Visualization Work: Difference between revisions
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*** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file. | *** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file. | ||
*** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here] | *** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here] | ||
** [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py merge_multi_PDBs_into_single_file.py] | |||
*** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder.. | |||
*** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model. | |||
** And more available [https://github.com/fomightez/structurework/tree/master/python_scripts here], with several of them demonstrated actively in Jupyter notebooks by launching 'binder' sessions from .[https://github.com/fomightez/cl_demo-binder here]. | |||
* In addition to my [https://github.com/fomightez/structurework/tree/master/python_scripts Python Scripts for Molecular Structure Analysis], my [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | |||
==Webserver for Python code== | |||
* Much of the more involved code featured for Spartan_Fixer is running in a webserver form [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything. | |||
== | ==Obtaining the Python Code== | ||
* | See [http://fomightez.github.io/ here] for getting my code in a form you can use on your machine or that you can modify. | ||
==Dockerfiles== | |||
* [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | |||
* [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | |||
==Related Python resources by others== | |||
*[https://github.com/samirelanduk/atomium atomium] is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ . | |||
*[https://github.com/rasbt/biopandas Biopandas] for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/. | |||
