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2024-05-18
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2024-05-17
Editing revision 5 of Calculation of the average structure and corresponding fluctuations
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/xplor/ saves the day : <code> structure @native.psf end dynamics analysis average asci=false input=fitted.dcd begin=0 skip=1 stop=2000000 reference=aver end write coordinates output=aver_and_rms.pdb end stop </code> The DCD file that you feed to /xplor/ *must* have global rotations-translations removed. Edit <b>aver_and_rms.pdb</b> and remove the header lines. Save the modified file. The B-factor column contains rms fluctuations for the corresponding atoms. View it : <code> rasmol aver_and_rms.pdb restrict not hydrogen cpk color temperature wireframe off cpk off cartoon </code> Use your editor to select the B-value column (ie the fluctuations) of the Cα atoms only and save them to file. Use /xmgr/ to make a graph of how the rms fluctuations change across the structure.
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