[PyMOL] FW: colouring states of a md trajectory

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:

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

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

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

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

[PyMOL] settings

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

[PyMOL] scenes and states

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.

Re: [PyMOL] scenes and states

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

Re: [PyMOL] settings

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

Re: [PyMOL] scenes and states

[[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 the

Re: [PyMOL] scenes and states

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 hans...@stolaf.edu wrote: [[sorry -- not used

Re: [PyMOL] settings

Thanks, Thomas On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder thomas.hol...@schrodinger.com 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.