Re: [cctbxbb] Error in fractional coordinates returned by cctbx

Peter, Thanks this is quite helpful! Andrew ----- Original Message ----- From: Petrus H Zwart Date: Thursday, December 28, 2006 5:19 pm Subject: Re: [cctbxbb] Error in fractional coordinates returned by cctbx

Hi David,

The fmod_positive doesn't work on a flex.vec3_double unfortunately.

The hack below does however work. It involves a python loop over the sites, which is not so nice of course. I wasn't able to find a python implementation of the coordinates.h class somehow. I hope this does the trick for now:

p1struc = icsd_structure.expand_to_p1() sites = p1struc.sites_frac() tmp_sites = flex.vec3_double() for site in sites: site = tuple(flex.fmod_positive(flex.double(site),1)) tmp_sites.append( site ) p1struc.set_sites_frac( tmp_sites ) p1struc.show_summary().show_scatterers() print "OK"

HTH

Peter

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Peter,

Thanks for the input... You are correct that for a protein mod(1) would be less than helpful. My issue is that without it I am unable to get the correct supercell structure of this and other inorganic crystals.

Is there a way via cctbx to get mod(1) values?

Thanks Andrew

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Hi Andrew,

I guess what happens is this:

When you use the expand_to_p1() command, the symmetry operators for P 32 2 1 are applied on the fractional coordniates as given. You expect a mod(1) operator to be carried out as well.

The advantage of not applying this operator is that you do not loose 'connectivity' between atoms. I can imagine that this is not a real issue for certain inorganic compounds, but for organic compounds and proteins not having

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'intuitive' connectivity in the coordinates (atoms close to each other are bonded) this is an issue.

I agree with Eric that the negative fractional do not fit in your view of a perfect world view either.

I guess Ralf/the cctbx has something somewhere to do the mod(1) operation to get the fractional coordinates in the range you

----- Original Message ----- From: Petrus H Zwart Date: Thursday, December 28, 2006 2:52 pm Subject: Re: [cctbxbb] Error in fractional coordinates returned by cctbx the like.

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HTH

Peter

----- Original Message ----- From: David A Carr Date: Thursday, December 28, 2006 10:59 am Subject: [cctbxbb] Error in fractional coordinates returned by

cctbx> > To: [email protected]

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Hello,

I have encountered the following inconsistency when working

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cctbx. The compound I am working with is as follows.

#Silicon Dioxide Quartz low. #Si O2 #ICSD Coll Number 62410

label="Si", site=(0.4643,0.0,0.6667) label="O", site=(0.411,0.2773,0.7783)

unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0",

space_group_symbol="P 32 2 1"

The error is can be seen in the below. In the second and

with third

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Si

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lines the z value is not a fraction of the unit. Similarly two of the oxygens are placed outside the unit cell. Why does cctbx place these outside of the unit cell?

Number of scatterers: 9 At special positions: 0 Unit cell: (4.843, 4.843, 5.348, 90, 90, 120) Space group: P 1 (No. 1) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si1 Si 1 ( 0.4643 0.0000 0.6667) 1.00 0.0000 Si1 Si 1 ( 0.0000 0.4643 1.3333) 1.00 0.0000 Si1 Si 1 (-0.4643 -0.4643 1.0000) 1.00 0.0000 O1 O 1 ( 0.4110 0.2773 0.7783) 1.00 0.0000 O1 O 1 (-0.2773 0.1337 1.4450) 1.00 0.0000 O1 O 1 (-0.1337 -0.4110 1.1116) 1.00 0.0000 O1 O 1 ( 0.1337 -0.2773 -0.4450) 1.00 0.0000 O1 O 1 (-0.4110 -0.1337 -0.1116) 1.00 0.0000 O1 O 1 ( 0.2773 0.4110 -0.7783) 1.00 0.0000

Below shows the expected fractional coordinates as expected. Based on the space group P 32 2 1.

0.4643 0.0000 0.6667 0.0000 0.4643 0.3333 -0.4643 -0.4643 0.0000 0.4110 0.2773 0.7783 -0.2773 0.1337 0.4450 -0.1337 -0.4110 0.1116 0.1337 -0.2773 -0.4450 -0.4110 -0.1337 -0.1116 0.2773 0.4110 -0.7783

Any insight into this would be of help. I am hoping to use cctbx as a part of our current software development project.

Thanks,

D.Andrew Carr [email protected]

# Below is the code that generates the error # posted above. #--------------------------------------------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex

def demo(): crystal_symmetry = crystal.symmetry( unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0", space_group_symbol="P 32 2 1") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer( label="Si", site=(0.4643,0.0,0.6667))) scatterers.append(xray.scatterer( label="O", site=(0.411,0.2773,0.7783))) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) print "ICSD Structure" icsd_structure.show_summary().show_scatterers() print icsd_structure.show_distances(distance_cutoff=2.5) print "Primitive" primitive_structure = icsd_structure.primitive_setting() primitive_structure.show_summary().show_scatterers() print p1_structure = primitive_structure.expand_to_p1() p1_structure.show_summary().show_scatterers() print print "Expanded to P1" icsd_structure.expand_to_p1().show_summary().show_scatterers() print "OK"

if (__name__ == "__main__"): demo()

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