- cctbxbb - phenix-online.org

real-space symmetry operators
by Nathaniel Echols 18 Aug '14

18 Aug '14

Hi all-- I'm trying to figure out how to orthogonalize symmetry operators given a unit cell, which doesn't seem to be something we have code for. These appear in PDB files in the REMARK 290 section but I haven't been able to find any other software that generates them, and the relationship between the symops and the real-space equivalents is unclear. I assume this is conceptually similar to orthogonalizing fractional coordinates, but unit_cell.orthogonalize() does not quite do what I wanted. In the PDB, for P63 it has this (excerpted): REMARK 290 2555 -Y,X-Y,Z ... REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 which looks like it should be relatively straightforward, but I'm not very good with matrices. Does anyone know the correct math for this? The corresponding rt_mx object from sgtbx looks like this: r=(0.0, -1.0, 0.0, 1.0, -1.0, 0.0, 0.0, 0.0, 1.0) t=(0.0, 0.0, 0.0) (Yes, I realize that there are much easier ways to apply symmetry operators to coordinates, but I want to limit the number of matrix multiplications involved when starting from Cartesian coordinates.) thanks, Nat

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Sphinx docs for CCTBX
by Nathaniel Echols 15 Aug '14

15 Aug '14

Thanks to some superb work by Nader Morshed, Oliver Zeldin, and Ian Rees, we now have automatically updated Sphinx docs for CCTBX: http://cci.lbl.gov/cctbx_docs/ Obviously these are still pretty sparse - right now most of the formal documentation is clustered here: libtbx libtbx.utils libtbx.phil (mostly re-using Ralf's old documentation) cctbx.miller iotbx.pdb (built on Ralf's newsletter article) mmtbx.command_line These are a combination of inline docstrings and separate restructured text files in cctbx_project/sphinx. We have automatically generated rst files for some modules, but others will need to be added manually. In the end I think we'll want to curate every file, but the current layout will get us started. To facilitate additional contributions, I've modifed the installation script for base packages to include a --sphinx option. After setting up CCTBX you can then do this: cd $BUILD libtbx.configure sphinx cd $SRC/cctbx_project/sphinx make html and you will get the full documentation built locally. I am still figuring out how to use Sphinx effectively; it is definitely possible to document Boost.Python extensions but it's not quite as obvious. I don't expect us to retroactively document several hundred thousand lines of code written over a decade, but if we can get the core parts thoroughly covered that will greatly reduce the barrier for new developers. Suggestions for particular modules to focus on are appreciated; I am going to try to cover the basic PDB+reflection file functionality. I encourage anyone doing CCTBX-related development to contribute as you go. (They don't need to be your own APIs, just modules you're reasonably familiar with.) Those of you who already have a ton of undocumented code can expect me to harass you periodically about fixing this. (Note that I've cannibalized at least one newsletter article for this, and continue to do so; we should re-use existing prose descriptions as much as possible without violating copyrights.) -Nat

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Re: [cctbxbb] resend
by Mustyakimov, Marat 24 Jul '14

24 Jul '14

Loop through symops: apply each symop to the original asu, then apply unit translations to minimize its distance to the original asu, test if new asu intersects with the target 27-bricks-large box, use it, if it does. Keep in mind that asu is not always a brick, it is always a convex polyhedron in cctbx. I do not see any good reason for doing all that. I do not read cctbxbb. On Jul 24, 2014, at 2:43 PM, Alastair Fyfe <afyfe(a)soe.ucsc.edu> wrote: >> Hi Marat, my apologies if this is a duplicate. From Pavel's comment it occurred to me you might not follow posts to the cctxbb >> Alastair >> ------ >> >> Many thanks for your replies. >> >> Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results >> back to unit cell thus obtaining a "full" unit cell (I expect >> "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap >> with the 26-brick neighborhood of the starting brick. This should work >> but seems inefficient. >> >> Marat: applying SymOps to the basis vectors seems a great idea. >> However, it wasn't clear to me how to combine sg SymOps to yield the >> 26 adjacent bricks. Does the map expansion code do this? >> >> >

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Re: [cctbxbb] 26-fold symm expansion of asu?
by Alastair Fyfe 24 Jul '14

24 Jul '14

Many thanks for your replies. Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results back to unit cell thus obtaining a "full" unit cell (I expect "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap with the 26-brick neighborhood of the starting brick. This should work but seems inefficient. Marat: applying SymOps to the basis vectors seems a great idea. However, it wasn't clear to me how to combine sg SymOps to yield the 26 adjacent bricks. Does the map expansion code do this? On 07/23/2014 12:00 PM, cctbxbb-request(a)phenix-online.org wrote: > Send cctbxbb mailing list submissions to > cctbxbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/cctbxbb > or, via email, send a message with subject or body 'help' to > cctbxbb-request(a)phenix-online.org > > You can reach the person managing the list at > cctbxbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cctbxbb digest..." > > > Today's Topics: > > 1. Re: 26-fold symm expansion of asu? (Pavel Afonine) > 2. Re: 26-fold symm expansion of asu? (Mustyakimov, Marat) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Jul 2014 18:58:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Cc: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <53CF16C8.5040504(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you > want and probably that would be what you call "slow". Could you please > explain some more what it is for and why, and may be give some context? > Perhaps that helps me to see if we have something similar already > available.. > > For instance we have very efficient code that computes maps in ASU, and > also that expands map in ASU into the whole P1 box. This is something > Marat wrote recently and is very efficient. May be you can reuse that or > at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: >> Hi, >> I'd be grateful for any pointers to clipper or cctbx code that >> addresses the following: given a "brick" of map grid coordinates that >> enclose the asu, obtain the 26 symmetry-related "bricks" which contact >> it. Calculating this by successively generating symmetry mates and >> testing seems slow; I was wondering whether there was a better way. >> thank you, >> Alastair Fyfe >> UCSC >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Jul 2014 14:01:13 +0000 > From: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > To: Pavel Afonine <pafonine(a)lbl.gov> > Cc: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <9457BEEC-4821-4BBB-8D91-E903AAFAE7F0(a)ornl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > The fast way to generate symmetry equivalent ASU: > Apply symmetry operation to unit vectors: ex = SymOp*(1,0,0), ey=SymOp*(0,1,0) and ez=SymOp*(0,0,1); > Then every map point of the symmetry related asu is obtained from the original one: > new_ijk = i*ex + j*ey + k*ez where (i,j,k) is the grid point in the original ASU. > > Marat Mustyakimov > P.O. Box 2008, Bldg. 8600, MS-6475 > Oak Ridge National Lab > Oak Ridge TN 37831 USA > e-mail: mustyakimovm(a)ornl.gov<mailto:[email protected]> > e-mail: marat.mustyakimov(a)gmail.com<mailto:[email protected]> > Tel: +1-865-253-3924 > > On Jul 22, 2014, at 9:58 PM, Pavel Afonine <pafonine(a)lbl.gov<mailto:[email protected]>> wrote: > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you want and probably that would be what you call "slow". Could you please explain some more what it is for and why, and may be give some context? Perhaps that helps me to see if we have something similar already available.. > > For instance we have very efficient code that computes maps in ASU, and also that expands map in ASU into the whole P1 box. This is something Marat wrote recently and is very efficient. May be you can reuse that or at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: > Hi, > I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. > thank you, > Alastair Fyfe > UCSC > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > ------------------------------ > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > > End of cctbxbb Digest, Vol 64, Issue 2 > **************************************

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26-fold symm expansion of asu?
by Alastair Fyfe 23 Jul '14

23 Jul '14

Hi, I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. thank you, Alastair Fyfe UCSC

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Phenix dependencies in CCTBX code
by Graeme.Winter＠diamond.ac.uk 22 Jun '14

22 Jun '14

Dear All, In cctbx_project/iotbx/pdb/multimer_reconstruction.py there is a dependency on Phenix from phenix.command_line.simple_ncs_from_pdb import simple_ncs_from_pdb from phenix.command_line.simple_ncs_from_pdb import ncs_master_params Please could someone remove this? I just had a look at cleaning things up so that this was encapsulated but was not obvious and figured risk of breaking was more substantial. This is breaking our nightly build tests at Diamond as we don’t check out phenix :o( Thanks Graeme -- 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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Phenix dependencies in CCTBX code
by Graeme.Winter＠diamond.ac.uk 22 Jun '14

22 Jun '14

Dear All, In cctbx_project/iotbx/pdb/multimer_reconstruction.py there is a dependency on Phenix from phenix.command_line.simple_ncs_from_pdb import simple_ncs_from_pdb from phenix.command_line.simple_ncs_from_pdb import ncs_master_params Please could someone remove this? I just had a look at cleaning things up so that this was encapsulated but was not obvious and figured risk of breaking was more substantial. This is breaking our nightly build tests at Diamond as we don’t check out phenix :o( Thanks Graeme -- 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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Re: [cctbxbb] Boost Import Error
by Magnus Andersson 19 Jun '14

19 Jun '14

Hi all, In case anyone else runs into the same problems (which is not unlikely), the following worked for me: > svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol > cd pymol > cctbx.python setup.py build > cctbx.python setup.py install > Thanks to Luc & Nat for being helpful and persistent! Cheers, Magnus > > On 17 Jun 2014, at 21:34, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > >> Hi, >> >> it's a bit late here in Paris but I can at least fix one point: >> >>> port select --set python27 >>> Error: The 'set' command expects two arguments: <group>, <version> >> >>> I tried to figure this out but without success... sorry to bug you with syntax issues. >> >> I'm the one to be sorry here as I pulled it from the top of my head and got it wrong. It's >> >> port select --set python python27 >> >> As for your original problem, I'll try to regroup and think through our former exchange to see what I may have missed. >> >> Best wishes, >> >> Luc >> >

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Boost Import Error
by Magnus Andersson 17 Jun '14

17 Jun '14

Hi, I've installed the cctbx package from the selfextracting file found in http://cci.lbl.gov/cctbx_build/ but I run into problems when importing cctbx in my python script: import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency ImportError: No module named boost.optional It is flex.py that wants to import boost.optional and does not find it. However, I find these three files: optional.hpp optional_fwd.hpp optional_io.hpp in the following directory: /Users/magnus/Downloads/cctbx_sources/boost/boost/optional which suggests that it's present. What am I missing here? I'm using Mac OS X Version 10.9.3 and Python2.7. Cheers, Magnus

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sparse matrix
by David Waterman 10 Jun '14

10 Jun '14

Hi, I have a problem where the use of a sparse matrix is appropriate, so I was pretty happy to grep cctbx for "sparse" and discover the code in scitbx/sparse. I'm just browsing through the code and tests to get a feel for how to use these types. In my existing Python code I set the values for some columns using flex.double vectors, then ultimately fill a flex.double(flex.grid(n,m)) by these columns using matrix_paste_column_in_place. It seems to me I can use a very similar pattern by replacing the flex.doubles with sparse.matrix_columns and setting columns in the sparse.matrix using slice notation: mat[:,0] = column. So far so good. The issue is that I'm not sure how best to go about setting the values in the matrix_column in the first place. At the moment I'm making a lot of use of flex.size_t selections and the set_selected method of flex.double to efficiently (from Python) set elements of one flex.double from another. It appears that there is no similar functionality for sparse.matrix_column. Am I right? Possibly the best I can do is construct a Python dictionary consisting of the indices from my size_t selection and the values from my flex.double array and use these to construct the matrix_column, as done in tst_sparse, e.g. sparse.matrix_column(m, {1:0.1, 2:0.2}). Without having tried this, I sense it might be a burden. I have a lot of values to set and don't really want to convert from flex.double via a dictionary. Are there any philosophical/technical/other reasons for not writing a set_selected method for sparse.vector? If not, I might try to do this. Thanks -- David

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