[PyMOL] FW: colouring states of a md trajectory

2013-06-03 Thread Sridharan, Sudharsan
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

Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

2013-06-03 Thread Troels Emtekær Linnet
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

Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

2013-06-03 Thread Tobias Beck
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

[PyMOL] settings

2013-06-03 Thread Robert Hanson
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

[PyMOL] scenes and states

2013-06-03 Thread Robert Hanson
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

Re: [PyMOL] scenes and states

2013-06-03 Thread Tsjerk Wassenaar
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

Re: [PyMOL] settings

2013-06-03 Thread Thomas Holder
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

Re: [PyMOL] scenes and states

2013-06-03 Thread Robert Hanson
[[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

Re: [PyMOL] scenes and states

2013-06-03 Thread Thomas Holder
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

Re: [PyMOL] settings

2013-06-03 Thread Robert Hanson
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