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
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