Now I have a problem, my PDB structure contains 4 chains. I want to remove 2 of them and the co- crystallized ligand, how can I do this if I'm following nearly the same steps as this tutorial ? https://galaxyproject.github.io/training-material/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html
The second problem is that there are missing residues in one of the chains, I tried modelling them in Chimera but I don't know how to keep the model of a certain chain with the other chain of the native PDB structure as 1 structure PDB file, can any one help me please?
Hi,
The first, you can do by opening your file with wordpad and eliminating the chains that you are not interested in. The second, it can be done by separating the chains in different PDB files and once you have the complete models, you can generate the oligomer by superimposing the complete models on your initial multimeric model, this latter you can easily perform with pymol.
To perform the first step, you can also use the visualizer of the Discovery studio.
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