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2024-04-18
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2024-04-17
Editing Calculation of rmsd from the average structure
/xplor/ to save the day : <code> structure @native.psf end coordinates disposition=comp @aver_and_rms.pdb evaluate ($first = 0) evaluate ($step = 1) evaluate ($current = $first) read trajectory asci=false input=fitted.dcd begin=$first skip=$step stop=20000000 end set display=aver_vs_MD.rmsd end while ($status # "COMPLETE") loop traj coor fit selection=(not hydrogen) end coor rms selection=(not hydrogen) end evaluate ($rms_ALL_ALL = $RESULT) coor fit selection=(segid="A " and not hydrogen) end coor rms selection=(segid="A " and not hydrogen) end evaluate ($rms_ALL_A = $RESULT) coor fit selection=(segid="B " and not hydrogen) end coor rms selection=(segid="B " and not hydrogen) end evaluate ($rms_ALL_B = $RESULT) coor fit selection=(name ca) end coor rms selection=(name ca) end evaluate ($rms_CA_ALL = $RESULT) coor fit selection=(name ca and segid="A ") end coor rms selection=(name ca and segid="A ") end evaluate ($rms_CA_A = $RESULT) coor fit selection=(name ca and segid="B ") end coor rms selection=(name ca and segid="B ") end evaluate ($rms_CA_B = $RESULT) display $current $rms_CA_ALL $rms_CA_A $rms_CA_B $rms_ALL_ALL $rms_ALL_A $rms_ALL_B evaluate ($current =$current + $step) read trajectory next end end loop traj stop </code> Then use something in the line of <code> xmgr -block aver_vs_MD.rmsd -bxy 1:2 -bxy 1:3 -bxy 1:4 xmgr -block aver_vs_MD.rmsd -bxy 1:5 -bxy 1:6 -bxy 1:7 </code> to view the results : [[image: rmsd from the average structure (xmgr)]]
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