- cctbxbb - phenix-online.org

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()

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Re: [cctbxbb] set_use_u_iso and set_use_u_aniso
by Ralf W. Grosse-Kunstleve 08 Jan '07

08 Jan '07

> > What are those methods of xray.scatterer for? > > And what are their relation to set_grad_u_iso and set_grad_u_aniso? You can use any combination of u_iso and u_star (anisotropic). We had to make this generalization to accomodate TLS refinement. I.e. there are four combinations, use_u_iso/use_u_aniso false/false, true/false, false/true, true/true. The total Debye-Waller factor is the product dw_iso * dw_aniso. If use_u_iso is false, dw_iso = 1, similarly dw_aniso = 1 if use_u_ansio is false. Unfortunately I didn't find the time yet to eliminate the anisotropic_flag, which is redundant. The main problem is that phaser needs to be changed in many places in order to get rid of the flag. The grad_u_iso and grad_u_ansio control the computation of the gradients. The flags are independent of corresponding use flags. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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set_use_u_iso and set_use_u_aniso
by Luc Bourhis 08 Jan '07

08 Jan '07

What are those methods of xray.scatterer for? Luc

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Re: [cctbxbb] Error in fractional coordinates returned by cctbx
by Ralf W. Grosse-Kunstleve 29 Dec '06

29 Dec '06

> We could add .mod_positive() and .mod_short() methods to flex.xray_scatterer, and > then the corresponding two-liners .sites_mod_positive() and .sites_mod_short() to > xray.structure. I'll put it on my to-do list. Done: http://cci.lbl.gov/cctbx_build/all.html Build 2006_12_28_2147 or later includes the new methods. E.g.: p1_structure = structure.expand_to_p1().sites_mod_positive() HTH, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [cctbxbb] Error in fractional coordinates returned by cctbx
by Ralf W. Grosse-Kunstleve 29 Dec '06

29 Dec '06

> flex.fmod_positive( coordinates, 1 ) > > on the fractional coordinates on your sites. > > Ralf, is there a better way? No, Peter's Python loop over the scatterers is currently the best solution. We could add .mod_positive() and .mod_short() methods to flex.xray_scatterer, and then the corresponding two-liners .sites_mod_positive() and .sites_mod_short() to xray.structure. I'll put it on my to-do list. Cheers, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Error in fractional coordinates returned by cctbx
by David A Carr 28 Dec '06

28 Dec '06

Hello, I have encountered the following inconsistency when working with 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 third Si 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 dcarr2(a)gmu.edu # 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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Re: [cctbxbb] Possible contributions to the cctbx
by Luc Bourhis 16 Dec '06

16 Dec '06

On 16 Dec 2006, at 06:53, Ralf W. Grosse-Kunstleve wrote: >> We have not developed those two features yet. Fair enough about the >> smtbx… We can easily mimic the mmtbx, > > I just wanted to say that you are most welcome to start the smtbx > tree under the cctbx SF probject. This is just an offer, I'd be > just as happy if you decide to start the tree somewhere else. Oh, I see! Sorry, I misunderstood you then. Thanks for the offer. It would make sense indeed. Of course, our ultimate goal is to develop the equivalent of Phenix for small molecules, and that would not live on sourceforge.net/projects/cctbx either. > It is technically very easy to leverage the cctbx build system for > other modules (I have at least 20 other modules floating around), > i.e. so that you can say libtbx/configure.py smtbx and you'll have > everything set up (PYTHONPATH, PATH, smtbx.python, etc.). The > problem is it is not documented enough (just Michael > Hohn's notes at http://cci.lbl.gov/~hohn/scitbx-tour.html). I hope > to find time to write more detailed web pages over the holiday break. I would highly appreciate that. By easy you probably mean it boils down to add a few instructions in a config file but my experience is that finding out those in the first place is not easy! Anyway, I am afraid I will come back to you with countless questions when I will start to develop with the cctbx. Thanks again, Luc

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Re: [cctbxbb] Possible contributions to the cctbx
by Ralf W. Grosse-Kunstleve 15 Dec '06

15 Dec '06

Hi Luc, > This is a spin-off from the thread about constrained hydrogen > refinement. On the todo list of our EPSRC project, we have a few more > items which I think would fit well in the cctbx. > > 1) anharmonic thermal displacements. Not only the Gram-Charlier ones > but also about the modelling of atoms disordered over a circle or a > line (as done in Crystals [1]). > > 2) multipolar scattering factors, for charge density studies. These suggestions look quite specific to small molecule crystallography. They make me think it would be best to have a "smtbx" (small molecule toolbox) module (inspired by David's message). Do you have a CVS or SVN repository already? Is it publicly accessible (read only)? Cheers, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [cctbxbb] constrained hydrogen geometry
by Ralf W. Grosse-Kunstleve 15 Dec '06

15 Dec '06

Hi Luc, > I was trying to figure out whether this interface would be sufficient > and/or necessary for the Hydrogen geometry constraints. I am not > quite sure I understand what is gradient_sum_matrix exactly in fact. gradient_sum_matrix is not directly relevant to the hydrogen problem. The only commonality is the chain rule. Roughly, if you have to variables x, y which are "normally" independent and have gradients df/dx and df/dy, and if under "special circumstances" x becomes a function of y (or vice versa), you have to add up the gradients according to the chain rule. If you work this out for the linear relations given by the symmetry operations, you can cast the result in the form of the "gradient sum matrices". Below is a simple example, by Peter Zwart, constraining the sum of occupancies to one. In the hydrogen case, I'd think you just write down the equations constraining the coordinates to each other. Then study them to apply the chain rule. Done! :) Regarding the interfaces: I usually think about interfaces after I've worked out the math and/or algorithms. It is good to make interfaces as similar as possible, but ultimately "form follows function", as a famous architect taught us. Most importantly, find class, function and variable names that convey meaning even to the "reader" no immersed in the problem. That's more than half the battle. > It is the philosophy of the cctbx, isn't it? You have constructed > the cctbx so as to use it as Python library, relegating C++ to some > sort of assembly language for efficiency. Yes, that's a good viewpoint. > The lack of abstraction in the C++ code of the cctbx I don't know what you mean. :) > (hardly any inheritance, Because it has a large potential for obfuscating what's going on. Inheritance is like salt in the soup. > no advanced genericity) You must have overlooked Boost.Python. :) If that doesn't change your mind, look closer at the implementation of the array algebra header files in scitbx/array_family, including the auto-generated header files in cctbx_build/include. > would require wrapping a lot of the cctbx classes behind > proxies inheriting from abstract types. I find this approach cumbersome and fruitless. I am a big believer in form follows function. Function follows form (design interfaces first) doesn't work for me. I always try to achieve first what I actually want to do, then find a good form for it. > A typical example for me are those classes dealing > with position constraints and ADP constraints. They > are unrelated in C++, cctbx::sgtbx::site_constraints and > cctbx::sgtbx::tensor_rank_2::constraints, although they have both have > the same member functions listed above. Functionally the member functions are unrelated, unless you can come up with a general engine that applies the chain rule automatically to a given function. (Such tools exist, e.g. adolc, but are heavy-duty.) I think it would be counter-productive to tie adp/site constraints code together just because the names of the methods are similar. I consider modularity a more important value. > Of course, from Python, it does not matter, thanks to duck typing: > if two objects answer the same method calls, then they are by all > practical means of the same type. The adp/site constraints are not a good example. We don't want to use them interchangeably. I've tried to use the "functor" idea (unifies interfaces without inheritance) in some places, but even that often turns out to be a struggle. This is especially the case when another person adds on (e.g. cctbx.xray.target_functors). What counts the most in my opinion is to avoid redundancy. That's my most important goal when writing source code, because redundancy hampers progress and multiplies bugs, among other bad things. I'm trying to use all tools available to cut back redundancy. I find both templates and inheritance invaluable and use them where they help reducing redundancy, but I do not see "use templates" or "use inheritance" as goals in their own right. > Our group would be more than happy to contribute them to the cctbx > since we absolutely need them for our project. That's great! I think you can achieve a lot quickly if you limit yourself initially to Python. If you then check in what you have, I'd be happy to walk you through the first few times moving time-critical functionality to C++. Cheers, Ralf By Peter Zwart: Some ideas on how to restrain sums of variables to unity. say we have f(a,b,c) with a(x1) = x1 b(x2) = x2 c(x1,x2) = 1 - x1 - x2 Say we have from the refinement engine the following numerical values (right hand side) for our partial derivatives: df/da = Ga df/db = Gb df/dc = Gc The chain rule says: dq/dx = (dq/du)(du/dx) + (dq/dv)(dv/dx) Thus df/dx1 = (df/da)(da/dx1) + (df/dc)(dc/dx1) = Ga - Gc df/dx2 = (df/db)(db/dx2) + (df/dc)(dc/dx2) = Gb - Gc This gives you the rule to go from the full set of derivatives to the reduced set of derivatives (for the general case): #-------------------------------------------------- def pack_derivatives( g_array ): result = g_array[0:g_array.size()-1 ] result = result - g_array[ g_array.size()-1 ] return result #-------------------------------------------------- You also need to go from a reduced set of parameters to the full set of parameters (for the general case): #-------------------------------------------------- def expand_parameters( x ): result = x.deep_copy() result = result.append( 1 - flex.sum(x) ) return result #-------------------------------------------------- This of course assumes that the 'last' variable is the non unique none during refinement. ____________________________________________________________________________________ Any questions? Get answers on any topic at www.Answers.yahoo.com. Try it now.

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Possible contributions to the cctbx
by Luc Bourhis 14 Dec '06

14 Dec '06

This is a spin-off from the thread about constrained hydrogen refinement. On the todo list of our EPSRC project, we have a few more items which I think would fit well in the cctbx. 1) anharmonic thermal displacements. Not only the Gram-Charlier ones but also about the modelling of atoms disordered over a circle or a line (as done in Crystals [1]). 2) multipolar scattering factors, for charge density studies. [1] L. Schröder, D.J. Watkin, A. Cousson, R.I. Cooper, and W. Paulus. Crystals enhancements: refinement of atoms continuously disordered along a line, on a ring or on the surface of a sphere. J. Appl. Cryst., 37:545–550, 2004. Best wishes, Luc

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