Tag: ChimeraX

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Visualizing biological macromolecules is a critical skill for students and professionals in the biological sciences. In this protocol, we demonstrate how to model the active site of the enzyme glucokinase using four freely available programs for molecular modeling. This tutorial highlights several steps of the protocol for each program, which…

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Open multi-file AlphaFold models | ChimeraX Recipes

# # Open AlphaFold database models for proteins larger than 1400 amino acids. # These calculated in 1400 amino acid segments every 200 amino acids due to # limitations (GPU memory) of the AlphaFold software. We load and align # the segment models. This produces many clashes. # # Opening…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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Ligand GNP bound in PDB entry 7obq ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

  The above 2D and 3D (Mol*) views of ligand interactions use quaternary structure derived from the PDB entry. Please note: Some chain IDs in the tooltip are followed by a number in square brackets. This number corresponds to the operation ID (mmCIF ‘oper_expression’) used to transform the chain. The…

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Alternative way to generate .PDBQT file for AutoDock Vina? : bioinformatics

For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have…

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PyMol – molecule export problem

PyMol – molecule export problem 0 Dear all, I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost – regions that in the PyMol session file are embedded into helices are now loops…

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