Re: [PyMOL] Transformation Matrices

[Jason V. <jas...@sc...>]

Jacob,

The easiest will be to use matrix_copy. All objects start out with
their object matrix set to the identity. One you drag them around or
move them through an alignment, their matrices change. You can then
easily copy one object's matrix onto another object.

Cheers,

-- Jason

On Thu, Dec 29, 2011 at 3:32 PM, Thomas Holder
<sp...@us...> wrote:
> 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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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
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