RE: [PyMOL] turn

[DeLano, W. <wa...@su...>]

> From: Mirek Cygler [mailto:mir...@br...]

> 	I wonder if there is a command equivalent to "turn" in=20
> molscript? I would
> like to show a cartoon view of my molecule with some=20
> sidechains. When I use
> "show cartoon" and include a selection of sidechains, they=20
> appear far from
> the backbone worm.

Turn off "smooth loops" and "flat sheets" using the cartoon menu or the
commands

set cartoon_smooth_loops=3D0
set cartoon_flat_sheets=3D0

> 	Can I change the name of the object after loading the=20
> molecule into PyMol?

No, but you can create an identical copy and delete the original.

load test1.pdb
create test2=3Dtest1
delete test1

> When I save the molecule can I also save the secondary=20
> structure assignments
> with it?=20

I wish...this is on the "to do" list.

> Is there a facility within PyMol to detect secondary=20
> structure
> automatically?

Sort of.  util.ss make an attempt at it, but the algorithm in
unvalidated (something I just cooked up one morning).  For publication,
I encourage users to obtain secondary structure assignment via an
accepted algorithm.

load test1.pdb
util.ss test1
show cartoon

- Warren