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2024-05-07
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2024-05-06
Editing revision 7 of Calculation of rmsd from the starting structure
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If you've used /carma/ to remove translations-rotations, then you already have seen a plot of the evolution of rmsd from the starting structure /vs./ time. A more complex example for a protein with 4 segments (A, B, C, D) is : <code> carma -fit -atmid "ALLID" native.psf native.dcd mv carma.fit-rms.dat ALL.dat carma -fit -atmid "ALLID" -segid " A " -segid " D " native.psf native.dcd mv carma.fit-rms.dat AD.dat carma -fit -atmid "ALLID" -segid " B " -segid " C " native.psf native.dcd mv carma.fit-rms.dat BC.dat carma -fit -atmid "ALLID" -segid " A " native.psf native.dcd mv carma.fit-rms.dat A.dat xmgr ALL.dat AD.dat BC.dat A.dat </code> giving something like : [[image: Calculation of rmsd from the starting structure (xmgr)]] You can do a far more gentle job /via/ the /xplor/ scripting language (try to understand the atom selection syntax) : <code> structure @native.psf end coordinates disposition=comp @starting.pdb evaluate ($first = 0) evaluate ($step = 1) evaluate ($current = $first) read trajectory asci=false input=native.dcd begin=$first skip=$step stop=2000000000 end set display=sidechain.rmsd end while ($status # "COMPLETE") loop traj coor fit selection=((resid 8 or resid 26 or resid 52 or resid 22 or resid 38\ or resid 45 or resid 48 or resid 37 or resid 15 or\ resid 19 or resid 41) and not (name CA or name C or\ name O or name HN or name HA or name N) and not hydrogen\ ) end coor rms selection=((resid 8 or resid 26 or resid 52 or resid 22 or resid 38\ or resid 45 or resid 48 or resid 37 or resid 15 or\ resid 19 or resid 41) and not (name CA or name C or\ name O or name HN or name HA or name N) and not hydrogen\ ) end evaluate ($rms = $RESULT) display $current $rms evaluate ($current =$current + $step) read trajectory next end end loop traj stop </code> where *starting.pdb* is a PDB containing the initial coordinates of the solute (after PSF generation).
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