Dear Researcher,
I am using PyMOL software to visualize the protein structure. I would like to make open/closed/helix or different conformational changes in protein during the catalytic mechanism. I would be glad if you could tell me how it proceeds, or it can be through X-ray crystallography only?
I do not have a biochemistry background but I have to learn this thing.
Thank you very much!
Hi Ganesh, I´m afraid you can´t do that with PyMOL only, you need coordinate files for the open and the closed conformations, that should be obtained experimentally (eg. through X-ray crystallography, Cryo-EM, etc.). Alternatively, you could run simulations of the open-closed dynamics with some molecular mechanics software. But if all you want is to make a figure that *just shows* how the conformational change *would be* according to what you *think* it is, you can use the "drag" function of PyMOL, which allows you to manually move/rotate any group of selected atoms. Of course that would be a *fake* conformational change, only for illustrative purposes!!
Hi Ganesh, I think you need two sets of structural data for each conformational structure if the protein has two conformations and has been experimentally determined. In Pymol, you can change the protein structure manually, but it will be fake changes.
Javier M González Husam Sabah Auhim thank you very much for your comments.
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