- cctbxbb - phenix-online.org

Re: [cctbxbb] cbflib_ext
by Ralf W. Grosse-Kunstleve 05 Jun '07

05 Jun '07

Hi Jon, Nick Sauter is working on the cbflib extension. He told me the current version is a very incomplete prototype, but that he expects to to have a more comprehensive extension around the end of this month. We are planning to move the source code (cbflib_adaptbx) to SourceForge where it will be freely available. Ralf ----- Original Message ---- From: Jon Wright <wright(a)esrf.fr> To: cctbxbb(a)phenix-online.org Sent: Thursday, May 31, 2007 4:30:38 AM Subject: [cctbxbb] cbflib_ext Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon ____________________________________________________________________________________ Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7

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cbflib_ext
by Jon Wright 31 May '07

31 May '07

Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon

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Re: [cctbxbb] mask calculation using mmtbx
by Ralf W. Grosse-Kunstleve 04 Apr '07

04 Apr '07

Hi Celine, The interfaces have changed a lot since we published the example in the newsletter. An updated version is available here: http://cci.lbl.gov/~rwgk/tmp/example_bulk_solvent_mask_2007_04_03_1806.py This is only the mask calculation. The rest of the functionality is incorporated in the f_model.manager (I think it is explained a bit in newsletter No. 5). Let me know if you are still having trouble getting the example to work with the latest cctbx version. Ralf ____________________________________________________________________________________ Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather

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mask calculation using mmtbx
by celine Besnard 03 Apr '07

03 Apr '07

Hi, I am trying to use the cctbx to calclate a mask given a pdb following the exemple given on a newsletter. I am using a windows version of the cctbx extracted from the bundle. But in the exemple, the mask is constructed using the masks.mask_utils function from mmtbx. But I cannot see this function in mmtbx.masks. Is there another function I can use to construct a solvent mask? Thanks for any help Celine Besnard

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How can I do FFT with scitbx.fftpack in python
by 张沈鹏(电子科大大三) 29 Mar '07

29 Mar '07

which function can do fft?the help information as below?but none can do fft........... >>> help(fftpack)Help on module scitbx.fftpack in scitbx: NAME scitbx.fftpack FILE f:\foryou\桌面\fft\cctbx\cctbx_sources\scitbx\scitbx\fftpack.py FUNCTIONS adjust_gridding(...) C++ signature: adjust_gridding(int, int) -> int C++ signature: adjust_gridding(int, int, int) -> int adjust_gridding_triple(...) C++ signature: adjust_gridding_triple(class scitbx::af::small<long,10>, int) -> class scitbx::af::small<long,10> C++ signature: adjust_gridding_triple(class scitbx::af::small<long,10>, int, classscitbx::af::small<long,10>) -> class scitbx::af::small<long,10>-- Hi , I'm Earth-Man.你好，我是地球人。欢迎访问我的博客:http://zsp.javaeye.com/ --张沈鹏

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How can I do FFT with scitbx.fftpack in python
by 张沈鹏(电子科大大三) 29 Mar '07

29 Mar '07

newbie-- Hi , I'm Earth-Man.你好，我是地球人。欢迎访问我的博客:http://zsp.javaeye.com/ --张沈鹏

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Assertion Error in twin target test
by Luc Bourhis 23 Mar '07

23 Mar '07

Hi all, I have modified the least square residual classes in cctbx/xray/ targets.h and cctbx.xray to handle refinement against F^2. In the subsequent tests, the following assertion failure cropped up. It does not feel to me my changes caused it… Luc libtbx.python /Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py approx_equal eps: 0.5 approx_equal multiplier: 10000000000.0 -0.510137170481 approx_equal ERROR 0 approx_equal ERROR Traceback (most recent call last): File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 540, in <module> run() File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 488, in run tst_ls_on_i() File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 95, in tst_ls_on_i assert approx_equal( (fdif_real-old_derivs[0][N_test])/fdif_real, 0, eps=5e-1) AssertionError

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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 **************************************************************************************************************************************************************

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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

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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

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