pymol-users

[PyMOL] How to show a ribbon of a loop with alternate conformations

[Schubert, C. [PRDUS] <CSC...@it...>]

Seemingly simple, but I can't figure it out: 
I modeled a loop in 2 alternate conformations and want to display both
of the conformations in a ribbon or cartoon. The selection "show ribbon,
prot and alt B" does not do the trick. The selection syntax must be
correct since "color red, prot and alt B; show lines prot and alt B"
works. I could show only the backbone atoms in a pinch, but that is not
really what I want. Hard to imagine that this is a limitation in PyMol
nobody noticed over the years.

Cheers

	Carsten

Re: [PyMOL] How to show a ribbon of a loop with alternate conformations

[Jason V. <jas...@sc...>]

Hi Carsten,

How about the following:

# create new structures using alt '' and alt 'a'
# and then alt '' and alt 'b'
create confA, yourProtein and (not alt 'b')
create confB, yourProtein and (not alt 'a')

# update representation
hide
show cartoons confA+confB

You can also repeat the name and use state flags to make a two-state protein.

Cheers,

-- Jason

On Tue, Apr 27, 2010 at 3:51 PM, Schubert, Carsten [PRDUS]
<CSC...@it...> wrote:
> Seemingly simple, but I can’t figure it out:
>
> I modeled a loop in 2 alternate conformations and want to display both of
> the conformations in a ribbon or cartoon. The selection “show ribbon, prot
> and alt B” does not do the trick. The selection syntax must be correct since
> “color red, prot and alt B; show lines prot and alt B” works. I could show
> only the backbone atoms in a pinch, but that is not really what I want. Hard
> to imagine that this is a limitation in PyMol nobody noticed over the years.
>
> Cheers
>
>         Carsten
>
> ------------------------------------------------------------------------------
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] how to use side chain helper only on some residues, but not on other residues in the same session

[chern <ch...@ua...>]

Hi,
 I want to use a command to show some main chain atoms (that make hydrogen 
bonds with my ligand),  but not all of them. When I use side chain helper, 
it hides all main chain atoms for different objects, no matter where I put 
the command, between the objects in the script etc.Is there a way to have 
one object with main-chain atoms, and another object-without them.

Maia 

Re: [PyMOL] how to use side chain helper only on some residues, but not on other residues in the same session

[Jason V. <jas...@sc...>]

Hi Maia,

Just turn on the setting for one of the proteins instead of globally.
If you type the following,
  set cartoon_side_chain_helper, on
it will turn it on for all objects.  So, try this instead
  set cartoon_side_chain_helper, on, protein1

Here's an example:

# fetch two proteins, 1cll and 1ggz
fetch 1cll 1ggz, async=0
align 1cll, 1ggz
# turn on helper for just 1cll
set cartoon_side_chain_helper, on, 1cll
# show all as cartoon
as cartoon
# show sticks for residues 40--60
# notice only side chain helper for 1cll
show sticks, i. 40-60

Cheers,

-- Jason

On Tue, May 11, 2010 at 10:49 AM, chern <ch...@ua...> wrote:
> Hi,
> I want to use a command to show some main chain atoms (that make hydrogen
> bonds with my ligand),  but not all of them. When I use side chain helper,
> it hides all main chain atoms for different objects, no matter where I put
> the command, between the objects in the script etc.Is there a way to have
> one object with main-chain atoms, and another object-without them.
>
> Maia
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120