February 2007 - cctbxbb - phenix-online.org

float error
by Alexander.Schiffer＠sanofi-aventis.com 27 Feb '07

27 Feb '07

Dear all, I am trying to detwin a dataset using mmtbx.xtriage but when I run the program with the following command: mmtbx.xtriage data.mtz n_residues=1341 log=detwin.log hklout=data_detwin.mtz symmetry.action=detwin symmetry.twinning_parameters.twin_law=-h-k,k,-l twinning.twinning_parameters.fraction=0.41 I get this message: Attempting to detwin data ------------------------- Detwinning data with: - twin law: -h-k,k,-l BE WARNED! DETWINNING OF DATA DOES NOT SOLVE YOUR TWINNING PROBLEM! PREFERABLY, REFINEMENT SHOULD BE CARRIED OUT AGAINST ORIGINAL DATA ONLY USING A TWIN SPECIFIC TARGET FUNCTION! Traceback (most recent call last): File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/xtriage.py", line 5, in <module> xtriage.run(command_name="mmtbx.xtriage", args=sys.argv[1:]) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/xtriage.py", line 691, in run out=log) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/massage_twin_detwin_data.py", line 330, in __init__ self.final_array = detwinner.detwin_it(alpha=self.params.symmetry.twinning_parameters.fraction) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/massage_twin_detwin_data.py", line 197, in detwin_it print >> self.out, "Detwinning the data with fraction %3.2f"%(alpha) TypeError: float argument required Any idea? Best regards, Alexander Build tag: 2007_01_24_2154 Red Hat WS 3 Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH S&MA Chemical Sciences Germany Structural Biology Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w: www.sanofi-aventis.de ************************************************************************************************************************************************************** Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier (Vorsitzender), Dr. Matthias Braun, Hervé Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert **************************************************************************************************************************************************************

2 1

Re: [cctbxbb] fractional coordinate expansion ... share occupancy
by Ralf W. Grosse-Kunstleve 06 Feb '07

06 Feb '07

Hi Andrew, > My question is what is the best method for generating the correct > distribution of atoms at these points. Naively, one would just > randomly select 30% of the shared points to be aluminums and set the > other 70% as silicon. I doubt that this is ideal. Short answer: there is nothing in the cctbx that would help you directly. I have a past as a zeolite person. My understanding was that the 30%/70% occupancy factors are a way to model spatial averages, as that's all you get from the diffraction experiment. How to handle the overlapping atoms depends highly on the context. E.g. in refinement I'd keep the overlapping atoms but constrain the coordinates to be identical. For graphical presentation I'd probably want to find a nice way to present the mixed occupancy, i.e. I wouldn't want to simply draw two crosses on top of each other. What is your context? Cheers, Ralf ____________________________________________________________________________________ Never Miss an Email Stay connected with Yahoo! Mail on your mobile. Get started! http://mobile.yahoo.com/services?promote=mail

1 0

Re: [cctbxbb] fractional coordinate expansion ... share occupancy
by Ralf W. Grosse-Kunstleve 05 Feb '07

05 Feb '07

Hi David, > I have provided an example compound with scatterer code below as you > will note the output has overlapping atoms and the resulting 58 points > are not enough to cover the chemical formula. What do I need to do to > fix this? Sorry, I don't understand the question. Could you please explain what you expect to see as the output? Ralf ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL

2 1

fractional coordinate expansion ... share occupancy
by David A Carr 02 Feb '07

02 Feb '07

Hello All, Thanks to Ralph's modification in January I have had success with cctbx. Now I have another question. Is there a method in the cctbx for dealing with shared occupancy coordinates? I have a compound where in the reduced cell the x,y,z coordinates for two different atoms are the same and a "sof" fraction is given. What is the best practice for handling such points? I have provided an example compound with scatterer code below as you will note the output has overlapping atoms and the resulting 58 points are not enough to cover the chemical formula. What do I need to do to fix this? Thanks, Andrew **************************************** Dr. D. Andrew Carr George Mason University dcarr2(a)gmu.edu ## ## The following example is ## Na9.52 (Al7.2 Si16.8 O48) (H2 O)5.88 ## DAC 1.12.07 ##--------------------------------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex def demo(): crystal_symmetry = crystal.symmetry( unit_cell="13.12,13.57,15.81,90.0,143.0,90.000000", space_group_symbol="C 1 2/m 1") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer(#element = "Si", label="Si1", site=(0.0042,0.2561,0.0965),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al1", site=(0.0042,0.2561,0.0965),occupancy=0.3)) scatterers.append(xray.scatterer(#element = "Si", label="Si2", site=(0.3442,0.1125,0.3278),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al2", site=(0.3442,0.1125,0.3278),occupancy=0.3)) scatterers.append(xray.scatterer(#element = "Si", label="Si3", site=(0.3497,0.1193,0.1355),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al3", site=(0.3497,0.1193,0.1355),occupancy=0.3)) #--------------------------------------------- # Oxygens #--------------------------------------------- scatterers.append(xray.scatterer(#element = "O", label="O1", site=(0,0.3203,0))) scatterers.append(xray.scatterer(#element = "O", label="O2", site=(0.4292,0.1372,0.2924))) scatterers.append(xray.scatterer(#element = "O", label="O3", site=(-.0283,0.3315,0.1491))) scatterers.append(xray.scatterer(#element = "O", label="O4", site=(0.5,0.1347,0.5))) scatterers.append(xray.scatterer(#element = "O", label="O5", site=(0.1993,0.2072,0.2422))) scatterers.append(xray.scatterer(#element = "O", label="O6", site=(0.308,0,0.0850))) scatterers.append(xray.scatterer(#element = "O", label="O7", site=(-.1454,0.1619,0.0205))) scatterers.append(xray.scatterer(#element = "O", label="O8", site=(0.256,0,0.289))) scatterers.append(xray.scatterer(#element = "Na", label="Na", site=(0.7235,0.2619,0.3904),occupancy=1.19)) scatterers.append(xray.scatterer(#element = "O", label="O9", site=(0.663,0.5645,0.7249),occupancy=0.47)) scatterers.append(xray.scatterer(#element = "O", label="O10", site=(0.304,0,0.686),occupancy=0.53)) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) icsd_structure.show_summary().show_scatterers() print icsd_structure.show_distances(distance_cutoff=2.5) print 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 "OK" if (__name__ == "__main__"): demo()

1 0