How to open pdb files in pymol

But I assume that there is a reason for not solving the entire structure by either group, and that reasond could very well be flexibility of the two domains.

This might sound scary coming from a fellow bioinformatician : small-angle X-ray scattering on the whole protein can give a good indication of the domain organization. The best way according to me is to copy and paste the x,y,z coordinates of all the atoms of amino acids of second pdb after opening it with wordpad, or gedit in linux or in any other text editing program to the first pdb after residues and save it.

As your first pdb was in pdb format, so after saving it, it will remain in pdb format. Just open it in Chimera or discovery studio and minimize it to resolve any bad contacts or clashes.

I hope this helps. The different parts of the proteins were crystallized for the different kind of study. For the protein-protein docking part I am not sure, but i performed a multiple structure homology modelling and performed Molecular Dynamics for the modeled structure.

I need your suggestion regarding homology modeling. Conceptually it looks fine but I want to know where I can go wrong? Does protein-protein docking can be used for validation of the predict model? The copy-paste option sounds good when you do it in chimera and join model option, but the problem is how you will be sure of relative orientation of these domains.

For that, you need a similar protein having crystal structure available. If not, then take aa from the end of first model and the start of second model, create homology models as well as ab-initio models. This part will give you an idea of the relative orientation of domains. For ab initio, Quark is the best, so far i know It's not quite clear what you did.

Do I correctly understand that you made a homology model of the full-length protein using the a homologous third protein? If that is true you can use it to align the two crystal structures and model the link between the two. No protein-protein docking needed. Note that this is still a model. If the protein has two separate domains the relative orientation may be context dependent.

That is it may change when the protein interacts with another protein. Regarding to your question " Does protein-protein docking can be used for validation of the predict model? Then you will go further study like drug design, in this case you can use Protein- protein docking.

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That works if you're just trying to open multiple PDB files, but many times we have an ensemble of structures in a single PDB file. Andrew Fowler Hi, I am a pymol user. Biochemistry Virtual Lab I Biochemistry is the study of the chemical processes in living organisms. Biochemistry Virtual Lab II Biochemistry Virtual Lab II deals with topics like enzymology, purification of plant pigments and natural products as well as estimation of iodine value and saponification value of fats and oils.

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