Re: [PyMOL] Series of general questions

[Andreas <an...@bi...>]

Tony, Gareth,

when I display sidechains only, I want to see the proline nitrogen.=20
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 cho=
ose
> > only the sidechain atoms instead of the sidechain+backbone.  In the g=
ood 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 in=
stead
> > 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.
>=20
> PyMOL distinguished between element types and PDB atom names.  For
> example,
>=20
> select all_oxygen, (e;o)
> select backbone_oxygen, (n;o)
>=20
> So to select sidechain atoms of an existing selection my_sel:
> select sidechain_of_my_sel, (my_sel & !n;n,c,o)
>=20
>=20
> Gareth
--=20
                    Andreas F=F6rster
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