Re: [PyMOL] Aligning states one at a time

[Thomas H. <sp...@us...>]

Hi Jordan,

you can first intra_fit the multi-state object and then align its first 
state to the input structure.

# this will fit all states to the first state
intra_fit multimodel

# align first state to input structure
align multimodel, input, mobile_state=1

http://pymolwiki.org/index.php/intra_fit
http://pymolwiki.org/index.php/align
(PyMOLWiki seems to be down at the moment?)

A nicer fit might be possible with theseus, which does a down-weighting 
of flexible parts of your structure.
http://www.theseus3d.org/

Regarding your question "is their a command that can add a bunch of 
states back together", there is "join_states" if you have psico 
installed. http://pymolwiki.org/index.php/Psico

Cheers,
   Thomas

Jordan Willis wrote, On 07/09/12 03:21:
> Hi Pymol!
> 
> I have a question about movies, but has nothing to do with the movie
> commands, so don't worry.
> 
> I have 750 states that are dumped directly into pymol where each
> "move"  from my modeling program, is a new state. I want to compare
> this to the input structure which only has one state.
> 
> If I align the 750 states to the 1 input, it sort of gives me a
> "global" fit that seems to be a consensus among all 750 states. What
> I would like however is each state to be aligned to my input
> structure separately. Then when I hit play I won't see such huge
> moves away from the input and a bad alignment.
> 
> My plan was to write a script that can do one of the following:
> 
> Make 750 states of the input structure even though they all will be
> the same and align state1 from the output to state 1 to the input.
> 
> or:
> 
> split all out to a separate object, align each one separately then
> zip up all the objects into one state.
> 
> Usually when I do this, there turns out to be some command that can
> do this for me. Does anyone know of an easier way of doing this? Or
> perhaps have some tips for me in my scripts? For instance, is their a
> command that can add a bunch of states back together?
> 
> Thanks so much, Jordan
> 
> PS. In the newest release of pymol for mac, I have noticed that when
> I click on a letter in the sequence (when the s option is toggled) it
> selects the entire chain rather than the individual amino acid.

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen