Hi Jacob,
regarding "alignto" and states' iter-relations, this has recently been
fixed in open-source pymol.
"align" and "super" both take arguments "mobile_state" and
"target_state" and also preserve states' iter-relations.
Example:
align 1d7q, 2oqk, mobile_state=7, target_state=1
The matrix you get like this:
print cmd.get_object_matrix('1d7q')
You can use this matrix with "transform_selection".
There is also "matrix_copy" command, but I haven't tried it with
multi-state stuff.
http://pymolwiki.org/index.php/Align
http://pymolwiki.org/index.php/Get_object_matrix
http://pymolwiki.org/index.php/Transform_selection
http://pymolwiki.org/index.php/Matrix_Copy
Cheers,
Thomas
Jacob Keller wrote, On 12/29/11 18:33:
> Dear List,
>
> I want to superpose a series of 30 states on another (single-state)
> model in the following way:
>
> --Superpose the best (closest-fitting) state first. (I know which one this is)
> --Output that transformation matrix
> --Transform other states by same matrix to preserve states' inter-relation.
>
> Is there some function that will output such a matrix, for input into,
> say, "transform_selection"?
>
> I have done this using the alignto command, but it ruins the states'
> interelations.
>
> Jacob
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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