“(resid 30 and resname “LYS”) or (resid 31 and resname “LYS”)” where the lysine of interest is residue 30 in one structure and residue 31 in the other. If the residue numbers differ between the two structures, a cumbersome, though simple workaround is to specify the residue name, or some other attribute that is different between the 2 structures, in addition to the number, e.g. Now you can type a list in the atomselect box, e.g. If you want to use only a portion of each molecule to align the structures, open the Sequence viewer:Īnd identify the residue ID numbers from each structure. If you want to use every atom from both structures, simply type “protein”. Specify the atoms you want to use in the text box in the upper left corner of the RMSD Calculator. You can use the Trajectory Tool to align structures too, but the Calculator actually changes the coordinates of the aligned structure so that you can save them, while the Trajectory Tool only changes the orientation of how the two molecules are displayed with respect to one another. Open the RMSD Calculator (NOT the RMSD Trajectory Tool): Bosco Ho has an alternative take on this task that is definitely worth a read. There is still potentially a lot of guesswork required to identify a good set of atoms for Step 3 below. When I say “easily”, I mean that this method does not require scripting.
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