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When working with more exotic file formats,
import and export
structures with OpenBabel.
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Possible side-chain rotamers or domain movements can be analyzed by sampling dihedral angles (internal coordinates),
while protein flexibility is best looked at in cartesian space by sampling loops
or using Bert de Groot's CONCOORD plugin (currently Linux only). Apply CONCOORD only to energy-minimized structures without bumps,
otherwise you may run into convergence problems.
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List
the properties of atoms to objects, including names, numbers and secondary structure,
count how many units are contained in a selection,
find differences between selections
, determine the first and last atom or object spanning a selection and sum up atom
masses. |
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Switch between perspective and parallel projection
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Some things are non-trivial. Nevertheless,
YASARA delivers the answer at the touch of the
'Experiment' button. During an experiment, YASARA takes over control and uses its
'artificial intelligence' to do various things in the right order. A message at the bottom will keep you informed. Some experiments accept additional parameters,
look at the example macros to see how it works.
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YASARA uses other programs to perform additional tasks,
here you can install them. |
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