well, my point was just that they seem to be orientation sensitive although I
didn't look at
entire script in any detail and that if you wanted to re-orient the fragment
you would have to
recalculate these. Nothing difficult but just easier if there was a script that
said something like
"put this thing here with this orientation wrt some prior fragment " ( no
absolute directions
at this point. )
----------------------------------------
> Date: Fri, 4 Jan 2013 15:52:13 +0100
> From: spel...@users.sourceforge.net
> To: marchy...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Building of the Carbon lattice
>
> Hi Mike,
>
> I simply measured x_shift and y_shift from a cyclohexane fragment. Use
> the graphical Builder or the "fragment" command to load stuff from the
> fragment library.
>
> PyMOL> fragment cyclohexane
>
> Cheers,
> Thomas
>
> Mike Marchywka wrote, On 01/04/13 15:44:
> > Where do you get the x_shift and y_shift values? I ended up writing a
> > program to
> > take bond lengths and directions relative to select coord systems to
> > generate periodic or
> > almost periodic things. Right now polyenes but extensible. Is there some
> > program that
> > does this easily? This allows me to write a simple TcL script and reorient
> > the whole
> > molecule by changing one parameter . I don't currently have a way to
> > include library
> > items, like say a methyl group, and I was debating about doing this in
> > python
> > but I wanted to have easy access to lapack etc for later extensions.
> > Thanks.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
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