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Writing a pdb file from an xray_structure object
by Claudia Millán Nebot 12 Dec '12

12 Dec '12

Hi everyone, i have been using the xray_structure_simple() method to get an xray.structure object from a pdb object and use it to perform some calculations on it, one of them being expand it to P1. After, i tried to write a new pdb out of this xray_structure in P1. For that purpose, i used the following method: cctbx.xray.structure.as_pdb_file(self, remark=None, remarks=[], fractional_coordinates=False, resname=None, connect=None) but using it both with the original xray structure and with the one on P1 I get very bad lookings pdbs, with incorrect formating, like that for the case of the one in P1: ATOM 1 PDB= PDB 1 12.330 -6.948 -40.820 1.00 19.26 N ATOM 2 PDB= PDB 2 49.988 55.370 3.948 1.00 19.26 N ATOM 3 PDB= PDB 3 36.092 30.710 93.483 1.00 19.26 N ATOM 4 PDB= PDB 4 55.370 49.988 175.123 1.00 19.26 N ATOM 5 PDB= PDB 5 30.710 36.092 85.587 1.00 19.26 N so i guessed that something must be wrong with the residues.... and went to check the code. That as_pdb_file method calls to iotbx.pdb.xray_structure.as_pdb_file(), and on that code i realised that as i was calling it whithout any resname, it was retrieving it from some information on the scatterers that could be wrong. Putting the value of resname to ALA, as a trial, produced almost the same output except for the name: ATOM 1 PDB= ALA 1 12.330 -6.948 -40.820 1.00 19.26 N ATOM 2 PDB= ALA 2 49.988 55.370 3.948 1.00 19.26 N ATOM 3 PDB= ALA 3 36.092 30.710 93.483 1.00 19.26 N ATOM 4 PDB= ALA 4 55.370 49.988 175.123 1.00 19.26 N ATOM 5 PDB= ALA 5 30.710 36.092 85.587 1.00 19.26 N Up to this point, i don't get what is wrong. It may be that i'm using a too simple method and without the correct parameters (xray_structure_simple()), as i guess part of the error is that the assignation of the types of atoms and residues is going crazy. There are other ways of performing this step from a pdb to an xray_structure and viceversa? Thanks in advance! Best regards, Claudia Millán (cmncri(a)ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain

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Documentation .... again
by Graeme.Winter＠diamond.ac.uk 12 Dec '12

12 Dec '12

Hi Folks, Been thinking some more about the old chestnut of documentation. The lack thereof is a well understood issue, and to be honest one which is not going to change any time soon as no one has the time to maintain a manual - this is fine and well understood. As a kind of "patch" for this I was wondering if it would be possible to have a forum where someone could ask for e.g. documentation for a currently undocumented function, which could then be added to the subversion in the code itself. For example: cctbx_project/cctbx/xray/structure.py ... def structure_factors(self, anomalous_flag=None, d_min=None, algorithm=None, cos_sin_table=False, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None): what is cos_sin_table for? with things like this there is the attitude that it is safe to ignore, however if we're writing code to guide people's experiments it would be good to be sure of this. Some simple documentation explaining this would be very useful. I'm definitely not suggesting (i) that anyone writes a manual or (ii) that all undocumented functions are suddenly documented, only that there is a mechanism set up that someone could ask about this and that someone who knows the answer could commit the changes to cctbx and then reply with the diffs - perhaps the way that stackoverflow works, or an email, or something really lightweight. Even this mailing list could be used I guess? I would be happy to help with this, though the above example is not one where I know the answer! Thoughts? Best wishes, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Structure factor calculation weirdness
by Graeme.Winter＠diamond.ac.uk 10 Dec '12

10 Dec '12

Hi Folks, Some confusion here at diamond - it seems that the amplitude of F(hkl) depends on dmin ---------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex # 14keV wavelength = 12.3984 / 14.0 spgroup = 'Fd-3m' latt = (5.4309, 5.4309, 5.4309, 90, 90, 90) atoms = [('Si', 0.125, 0.125, 0.125)] allscatterers=[] for atom in atoms: allscatterers.append(xray.scatterer( label = atom[0], site = (atom[1], atom[2], atom[3]), u = 0)) structure = xray.structure( special_position_settings = crystal.special_position_settings( crystal_symmetry = crystal.symmetry( unit_cell = latt, space_group_symbol = spgroup)), scatterers = flex.xray_scatterer(allscatterers)).expand_to_p1() for dmin in 5.0, 2.5, 1.7: print dmin f_calculations = structure.structure_factors( d_min = dmin).f_calc().amplitudes().show_array() --------------- Chopped out only 001, 010, 100 from this... 5.0 (0, 0, 1) 0.290277589693 (0, 1, 0) 0.290277589693 (1, 0, 0) 0.290277589693 2.5 (0, 0, 1) 0.0 (0, 1, 0) 0.0 (1, 0, 0) 0.0 <snip> 1.7 (0, 0, 1) 0.278378587828 (0, 1, 0) 0.278378587828 (1, 0, 0) 0.278378587828 <snip> Have we misunderstood something? Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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UB matrix in cbf files
by Carlo.Vecchini＠diamond.ac.uk 04 Dec '12

04 Dec '12

Hello, I would like to add the orientation matrix information in the cbf file. Following the description in sections 3.2.2.2.3 of IUCr (G), I added the following lines in the cbf header: _diffrn_orient_matrix_type ub_matrix_test _diffrn_orient_matrix_UB_11 0.083424 _diffrn_orient_matrix_UB_12 -0.076007 _diffrn_orient_matrix_UB_13 -0.078787 _diffrn_orient_matrix_UB_21 -0.103374 _diffrn_orient_matrix_UB_22 -0.075939 _diffrn_orient_matrix_UB_23 -0.01146 _diffrn_orient_matrix_UB_31 -0.034434 _diffrn_orient_matrix_UB_32 0.043832 _diffrn_orient_matrix_UB_33 -0.156476 When I try to read back the values with: get_orientation_matrix() I get the following error: UBm = cbf_handle.get_orientation_matrix() File "~/CCTBX/cctbx_plus_build/lib/pycbf.py", line 3915, in get_orientation_matrix return _pycbf.cbf_handle_struct_get_orientation_matrix(self) Exception: CBFlib Error(s): CBF_NOTFOUND If I use set_orientation_matrix() to write the cbf file, I get a similar error. Does anyone have any suggestion on how to solve this? Thanks in advance, Carlo Vecchini -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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CBF compositing
by Frank Murphy 03 Dec '12

03 Dec '12

Hello, Does anyone have a CCTBX-based method for compositing multiple CBFs to a single image a la merge2cbf? Thanks in advance, Frank Murphy

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OS X Lion + CCTBX + scipy
by Graeme.Winter＠diamond.ac.uk 01 Dec '12

01 Dec '12

Hi Folks, Has anyone got scipy to build against the cctbx python binary distribution on OS X Lion? I am finding that it keeps on compiling some bits of the library for PPC architecture which does not work... Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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SVN broken?
by Jan Marten Simons 24 Oct '12

24 Oct '12

Hi, while trying to update to the latest svn revision or when trying a fresh checkout I encounter this error: svn co https://cctbx.svn.sourceforge.net/svnroot/cctbx/trunk cctbx_project svn: Can't find a temporary directory: Internal error According to a quick web search the problem is most likely on the svn server (either no disk space or corrupted .svn dir). Hopefully either sourceforge or any of you can fix this. Cheers, Jan

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Re: [cctbxbb] Question about sigma(I) calculation in merge_equivalents
by Kay Diederichs 21 Oct '12

21 Oct '12

Dear Keitaro, Phil, Luc, after looking into the question of how to merge equivalent reflections (in the context of XDS data processing), I am now convinced that cctbx should _not_ use max(internal sigma, external sigma) by default. Why? - it is not obvious to the "end user" of the data that come out of cctbx that this formula was applied (I am not aware that the above formula is clearly documented) - the data processing programs that I know of do not use this formula, but rather use the "external sigma" . I don't imply that the "external sigma" is better, but it violates the principle of least surprise to deviate from a proven procedure. - if the observations (that are merged in cctbx) come from one of these data processing programs then there is a chance that the error model was already adjusted such that the reduced chi**2 is near 1 (at least this is the case for XDS and SCALA). If the sigmas of the merged data then are adjusted upwards again (by the formula above), I have a strong feeling that this leads to an inconsistency. - using max() seems like an ad-hoc way and it lacks a clear rationale. I would like to see examples of comparison of downstream crystallographic calculations (most importantly, experimental phasing) using different ways of calculating the sigma of the merged data. Until this proves the superiority of the above formula, I believe it should be an option, not a default. thanks, Kay > Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp > Thu Sep 6 09:20:34 PDT 2012 > > Previous message: [cctbxbb] Question about sigma(I) calculation in > merge_equivalents > Next message: [cctbxbb] Question about sigma(I) calculation in > merge_equivalents > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > Dear Luc, > > Thank you for your explanation! I understand better than before. > > Usually, sigmas given by data processing programs are already > corrected based on their error model. > Sigmas are adjusted to match the actual scatter. > I think using internal variance is re-correction of sigmas. > Is it valid way? If internal variance is bigger, it suggests error > model is not perfect? > > I calculated external/internal variances using lysozyme (standard > sample in protein crystallography) data. > Intensities and sigmas are determined by XDS. > > I attached two plots, where "Imean", "wsigma", "sigma" are averaged > intensity, internal sigma, external sigma, respectively. > One plot is histogram of wsigma/sigma by multiplicity. For lower > multiplicity, we can see extreme discrepancies. (Note that each > vertical axis is not on the same scale.) > The other plot is wsigma/sigma vs intensity. Extreme discrepancies can > be seen in lower intensities. > I hope it could be interesting for you. > > > > Crystals use only the external variance by default, the reasoning > being that the internal variance being based on sample statistics is > almost always too unreliable because groups of equivalent reflections > are too small. > > Then, I think it would be nice if we can choose the way in cctbx. > I mean, option to choose "use bigger one" or "always use > external/internal variance" would be nice to have. > > I am looking forward to your comment. > > Best regards, > Keitaro > > 2012/9/6 Luc Bourhis <luc_j_bourhis at mac.com>: > > Dear Keitaro, > > > >> But it is still unclear to me why it takes the greatest of the > >> "internal" variance and "external" variance. > >> Is it based on some tests using real data? or is it theoretically > >> superior to using always external variance? > > > > Those are good questions and to be honest I do not know for sure the > answer to them. As it seems common in applied statistics, the treatment > starts with by-the-book methods relying on a well defined theory but at > the end there is always a completely heuristic twist. Particularly true > in crystallography I would argue. But let me try to give some rationales. > > > > It seems to me that the internal and external variance should not > differ too much. Let's consider the two ways this may not be true. > > > > 1. The quoted intensities of a group of equivalent reflections have a > small spread, leading to a small internal variance, but the quoted > sigma's are comparatively big, resulting in an external variance > significantly bigger than the internal one. This is a possible event but > an unlikely one: the statistical intuition in that case is to say that > the small internal variance is a fluke and to use the external one instead. > > > > 2. An external variance significantly smaller than the internal one, > should ring an alarm bell. Indeed a small external variance means that > the small quoted sigma's strongly suggests the intensities cannot spread > too much from their assumed common true value whereas the comparatively > bigger internal variance blatantly contradicts that. Thus either the > intensities or the sigma's have not been correctly determined. > Crystallographers seem to err on the side of trusting data here, i.e. to > disregard the sigma's, and therefore to choose the internal variance. > > > >> I would like to know how this method affects further > crystallographic process. > > > > I am afraid I do not have experience with your domain, protein > crystallography. I know that the small molecule program Crystals use > only the external variance by default, the reasoning being that the > internal variance being based on sample statistics is almost always too > unreliable because groups of equivalent reflections are too small. Since > Crystals is as well accepted as ShelXL to produce publishable > structures, it answer your question in at least in one corner of > crystallography, unfortunately not yours. > > > > I think it could be a simple and interesting exercise to take a > representative protein dataset of yours, then to print the redundancy, > the internal, and the external variance. Actually I would be surprised > if such a study has not already been done and published. Perhaps some of > the gurus on this forum can shed more lights onto that subject. > > > > Best wishes, > > > > Luc -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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FYI: The Quaternion Characteristic Polynomial method
by Jeffrey Van Voorst 19 Oct '12

19 Oct '12

Greetings, If you already know about the quaternion characteristic polynomial method for a fast closed-form solution of the least squares superposition problem, this note is mostly noise. While in the process of updating links to my project, I noticed the note at the bottom of the cctbx sourceforge page (http://cctbx.sourceforge.net/). I like the historical nature presented, and I used the historical method to numerically solve quartic polynomials in a previous project at Michigan State University that ranks relatively large datasets of protein small-molecule binding sites (with respect to a given query site). The superposition method I used has a closed form and is due to BKP Horn. Later on (after writing my dissertation), I found that using the historical method to numerically solve quartic polynomials is not numerically stable or robust. Fortunately, there is an easy solution, and if you are interested in a fast closed-form solution for the least squares superposition problem you would do well (in my opinion) to visit http://theobald.brandeis.edu/qcp/. Best regards, Jeff Van Voorst

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--enable-boost-threads flag
by Jeffrey Van Voorst 19 Oct '12

19 Oct '12

Greetings, If someone knows the answer off the top of their head, I would be interested in the answer. Otherwise, feel free to ignore this. Does the --enable-boost-threads flag for cctbx_sources/libtbx/configure.py do anything drastic besides include -pthread in the compiling and linking steps? I am trying to understand why I would get a free() error (for the shared_ptr to root_data) under the following situation: *) the iotbx_pdb shared library is configured without the --enable-boost-threads flag (on a linux box) *) sometimes reproducible from a test C++ program that is linked using -pthread even in the case when the program is as simple as loading a pdb file and creating the hierarchy. *) gcc 4.4.5 --Jeff Van Voorst

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