Hello.. I am working on iron sulfur clusters in the photo-system I, After optimizing the clusters the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix, when I tried to get this matrix using pymol, I got an error and I can't figure out the problem because I am new to pymol.
please, could anyone help me how to get the transformation matrix?
and also how to apply it to get the original coordinates ?
get_view returns the current viewing transformation matrix, set_view returns to those transformations. However, if you object coordinate system has been changed by some external processing, this will not help you.
You might load both your pre-processing and post-processing objects, and do a least-squares fit to align the post-processing object onto the object described by the original coordinates.
thx Annemarie, for your reply.
here what I did ..
using pymol
1- I loaded post and pre - processing object
2- I aligned them together
3- I tried to get the transformation matrix with this command
print cmd.get_object_matrix("pre-processing object")
and this step returns a 4*4 matrices
(-0.017042629420757294, 0.6273888349533081, -0.7785196304321289, -27.565351122804373,
0.15071848034858704, 0.7713475823402405, 0.6183096766471863, -142.13367787636093,
0.9884297847747803, -0.1067996621131897, -0.10770488530397415, -81.02178268868633,
0.0, 0.0, 0.0, 1.0)
I am not sure if this is the right way or not ?
and if it is right what should I do in order to apply it to the post-processing object ? should I apply is as it is or the inverse of it ?
You load the pre-processing object. I f you check its matrix, it should be the unit matrix (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0).
you load your post-processing object and align it to the pre-processing object (Careful - depending on the alignment command you use, either the first or the second parameter is the mobile object in the alignment process, pymol is not very consistent in this) - the pre-processing object should keep the unit matrix, while the matrix of the post-processing object would be the matrix that will bring your post-processing object back into the same coordinate system as the pre-processing object if you multiply its coordinates by that matrix.
thx a lot Annemarie,
so I used this command to apply the matrix ...
cmd.transform_object( "post_processing object", [-0.017042625695466995, 0.15071852505207062, 0.9884297847747803, 101.03673254990264, 0.6273888349533081, 0.7713475823402405, -0.10679969936609268, 118.27556096672724, -0.7785196304321289, 0.6183096766471863, -0.10770490765571594, 57.69601938212094, 0.0, 0.0, 0.0, 1.0])
am I doin it in a correct way ??
and I need to find the transformed structure, how I could do it ?
When you save the aligned structure as pdb, it should be saved with the transformed coordinates:
save pre_processing_object.pdb, pre_processing_object
save post_processing_object.pdb, post_processing_object
when you reload the two pdbs in a new PyMOL session, they should be loaded in the aligned relative orientation.
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