Can this plugin solve it:
http://www.pymolwiki.org/index.php/Rotamer_Toggle
Note, that you have to collect the script yourself, and replace
the original pymol menu.py file.
Not a easy solution to problem.
Note, it the script: http://www.pymolwiki.org/index.php/Rotkit
You can mutate through a command line, and selecting which
rotamer to use. But that would not solve your problem of specifying which
plane
to select.
In http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis
are some more examples of mutating in PyMOL and get the pKa
for the mutations.
Best
Troels
2011/12/8 Martin Hediger <ma....@bluewin.ch>
> Dear PyMOL List
> I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation
> of tryptophan to phenylalanin. If the sidechain is mutated from W to F,
> its reasonable to assume that the plane of the phenyl moiety of F
> would/should/could/might lie in the same plane as the indol part of the
> W if there was such a protein.
> Would it be possible to scriptically adjust the F side chain, after
> mutation, such that it lies in the W plane?
> Of course, this becomes ambiguous when, say, a A is mutated to a D,
> because what would then be the reference for the D side chain? However,
> N to D would be another case, where it would be desired to have the D
> end group be in as much overlay with the former N end group as possible.
>
> Any ideas on how this might be afforded? Probably not a one-liner though.
>
> Kind regards
> Martin
>
>
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