Hi Tsjerk,
Many thanks for pointing this out. Thanks to the spectrum_states script authors
as well. It worked perfectly!
Kind regards,
Sid.
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: 02 June 2013 20:34
To: Sridharan, Sudharsan
Cc: pymol-users@lists
Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packe
Hi Troels,
Many thanks for your email!
I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?
>svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>sv
I'm trying to understand settings. I see that there are at least these
levels of settings:
- global
- object
- state
- unique atom/bond
Are there more?
I'm unclear on when one overrides another. It looks to me that the general
"getSetting" methods have the option of up to three levels of setting
Questions:
Can two objects be in two different states -- object1 in state 3 and
object2 in state 10, for instance, at the same time? If so, how is that set
up? How is that then incorporated into a scene?
Do CGO, measurements, mesh, and volume objects have states as well?
Bob
--
Robert M. Hanso
Hi Bob,
The answer is yes to all.
fetch 1ubq, state=3
fetch 6lzm, state=10
cmd.load_cgo([7.0,0,0,0,2],name="sphere",state=2)
The representations (e.g. surface) do have states in the sense that the
each state gives a different surface. But whether the surface is shown or
not is controlled globall
Hi Robert,
you got the levels right.
The cmd.get method actually doesn't support querying atom level settings, even
though you can set them with cmd.set.
Atom settings are not state specific, unless you have a discrete object.
Scenes do not store settings, so using spectrum_states overrides sc
[[sorry -- not used to a list that requires "reply-all" to go back to the
list]]
What you describe there is a way to load a specific file into a specific
state, I think. I meant, once you have a set of multi-state objects, can I
select to compare two different states, one from one and one from th
Hi Bob,
it's the object-level "state" setting:
fetch 1nmr 1d7q, async=0
set state, 3, 1nmr
set state, 10, 1d7q
And since scenes do not store settings, this cannot be stored with a scene.
Cheers,
Thomas
On Jun 3, 2013, at 10:41 AM, Robert Hanson wrote:
> [[sorry -- not used to a list that r
Thanks, Thomas
On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder wrote:
> Hi Robert,
>
> you got the levels right.
>
> The cmd.get method actually doesn't support querying atom level settings,
> even though you can set them with cmd.set.
>
I see. That's helpful.
>
> Atom settings are not sta
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