![]() Go Go to the graphics screen and click off MOL1 and click on/off MOL2įilname. Shoall Display what we have done in a third object on theĬ (This will be MO元 on the graphics screen) Go Go to the graphics screen and click MOL1 on/offĭebump Find a rotomer that has the fewest bumpsģ Default %colzns Color the debumped residue also Shoall Display what we have done in a second object 2aĢ (This will be MOL2 on the graphics screen) Go Go to the graphics screen and look at your moleculeĬHAT Click the green box to return to command screenĪrg %colzns The percent is because we are not in the color menuġ3 just now. You will be prompted to select a group, which is readily made by clicking on any atom of the desired amino acid. To initiate a mutation, simply click on the mutation tool located at the top of the display window. This can be very useful to quickly evaluate the putative effect of a mutaion before actually doing the lab work. Shoall Display what we have done in object 1a Swiss-PdbViewer allows to browse a rotamer library in order to change amino acids sidechains. It might be tempting to mutate this residue, but remember. Could anyone give a hint on how to do it Thanks Fabio. You will see that the peptide is folded around a central tryptophan residue. Right now, I am not concerned about the possible rotamers of lysine, any lysine rotamer would work. (Substitute your PDB file for 1crn.pdb and the number of the residue you want to mutate for 13 used in this example.)Ĭolzns Color one residue (by zone) so you can see it For example, load test.pdb, mutate all residues to lysine and then save the mutated version to testK.pdb 2) the script would need to perform this task for all the pdb files in a directory. Open whatif and give the following commands.
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