Tony, Gareth,
when I display sidechains only, I want to see the proline nitrogen.
After I've loaded all objects, I select all mainchain atoms (except
proline nitrogen) and display sidechains like this:
select mainchain, n;C,O,N and not pro/n
show sticks, object and not mainchain
The advantage is that the mainchain selection works for all objects that
have been read into pymol before selection, like so:
show sticks, object2 and not mainchain
show sticks, object3 and not mainchain
etc
Andreas
> > 2) When selecting specific sidechains, it is often preferable to choose
> > only the sidechain atoms instead of the sidechain+backbone. In the good ol'
> > molscript days you would say select and not c or n or o but if you do that
> > in pymol it thinks you mean all carbon, nitrogen, and oxygen atoms instead
> > of their id in the PDB file. I'm sure this is worked out but I don't see it
> > in the example scripts I've found on line.
>
> PyMOL distinguished between element types and PDB atom names. For
> example,
>
> select all_oxygen, (e;o)
> select backbone_oxygen, (n;o)
>
> So to select sidechain atoms of an existing selection my_sel:
> select sidechain_of_my_sel, (my_sel & !n;n,c,o)
>
>
> Gareth
--
Andreas Förster
Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
Salt Lake City, UT 84132, phone: 001.801.585.3919
home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
http://www.biochem.utah.edu/~andreas
