coordinates -> space group + matrices
This is probably a simple (maybe stupid) question, but that never stopped me before: I want to give cctbx a set of primitive vectors and coordinates (cartesian or fractional), and have it return (1) the space group and (2) all the symmetry matrices. For example, given R = [4 0 0 % primitive vectors 0 4 0 0 0 4] x = [0.00 0.0 0.00 % fractional coordinates 0.51 0.51 0.51 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.50] I want cctbx to tell me this is space group #160 R3m, that there are 6 symmetry operations, and give me the corresponding matrices. This sounds easy, given everything cctbx can do, so it must be possible. Is there a simple example anywhere? Thanks. -- Kristopher E. Andersen http://www.physics.nau.edu/~andersen/ Northern Arizona University [email protected] Department of Physics and Astronomy (928) 523-7202
Kris Andersen wrote:
This is probably a simple (maybe stupid) question, but that never stopped me before:
I want to give cctbx a set of primitive vectors and coordinates (cartesian or fractional), and have it return (1) the space group and (2) all the symmetry matrices.
For example, given
R = [4 0 0 % primitive vectors 0 4 0 0 0 4]
x = [0.00 0.0 0.00 % fractional coordinates 0.51 0.51 0.51 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.50]
I want cctbx to tell me this is space group #160 R3m, that there are 6 symmetry operations, and give me the corresponding matrices.
Hello, Looks like the "F3m" setting, assuming all atoms are the same? Would you want to keep that or would you prefer it on the trigonal or hexagonal axes? Not sure if cctbx whether has a find symmetry algorithm, but there are a couple of other possibilities. Ton Spek's Platon software will read a structure in a cif file in space group P1 and then try to find the correct space group for you. Also there is Harold Stokes findsym program (http://stokes.byu.edu/findsym.html). Good luck, Jon
This sounds easy, given everything cctbx can do, so it must be possible. Is there a simple example anywhere?
Thanks.
-- Kristopher E. Andersen http://www.physics.nau.edu/~andersen/ Northern Arizona University [email protected] Department of Physics and Astronomy (928) 523-7202
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Jon, thanks for your reply. I'm familiar with findsym, but it doesn't (to my knowledge) give the space group operations. What I'd like is something to find the space group and then give the symmetry operations in the basis of my coordinates (or a way to transform my coordinates into the basis of the symmetry matrices). I was hoping it may be possible to put together elements of the ccbtx library to do this easily? P.S. In my haste to come up with an example that wasn't totally trivial, I forgot to mention I was thinking in terms of the atoms being different, hence the R3m symmetry. The example was suppose to be for a perosvikite. On Sep 17, 2007, at 11:33 PM, Jon Wright wrote:
Kris Andersen wrote:
This is probably a simple (maybe stupid) question, but that never stopped me before:
I want to give cctbx a set of primitive vectors and coordinates (cartesian or fractional), and have it return (1) the space group and (2) all the symmetry matrices.
For example, given
R = [4 0 0 % primitive vectors 0 4 0 0 0 4]
x = [0.00 0.0 0.00 % fractional coordinates 0.51 0.51 0.51 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.50]
I want cctbx to tell me this is space group #160 R3m, that there are 6 symmetry operations, and give me the corresponding matrices.
Hello,
Looks like the "F3m" setting, assuming all atoms are the same? Would you want to keep that or would you prefer it on the trigonal or hexagonal axes? Not sure if cctbx whether has a find symmetry algorithm, but there are a couple of other possibilities. Ton Spek's Platon software will read a structure in a cif file in space group P1 and then try to find the correct space group for you. Also there is Harold Stokes findsym program (http://stokes.byu.edu/findsym.html).
Good luck,
Jon
This sounds easy, given everything cctbx can do, so it must be possible. Is there a simple example anywhere?
Thanks.
-- Kristopher E. Andersen http://www.physics.nau.edu/~andersen/ Northern Arizona University [email protected] Department of Physics and Astronomy (928) 523-7202
_______________________________________________ cctbxbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/cctbxbb
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Hi I have a question about solvent mask in cctbx. I generated a mask using the mask manager. Then I am calculating the structure factors from the mask (using mask_manager.structure_factors() ). If I am trying to redo a map from the calculated structure factors (outside the cctbx and I hope without any scaling), I get a map with a mean density of zero, which is not the case of the original mask. I suppose that the structure_factors() function is doing some scaling at some point. In the source codes of the function structure_factors , I found scale = miller_set.unit_cell().volume() / matrix.col(fft_manager.n_real()).product() map_of_coeff *= scale from_map = maptbx.structure_factors.from_map( miller_set.space_group(), anomalous_flag, miller_set.indices(), map_of_coeff, conjugate_flag) But I don't understand what the "scale line" is doing. So I wonder what is exactly this matrix.col(fft_manager.n_real()).product() doing? And how do I generate structure factors for a mask without any scaling? Thanks for any help Celine
participants (3)
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celine Besnard -
Jon Wright -
Kris Andersen