[cctbxbb] How to load a structure from a .cif file?

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Mon Dec 13 09:21:47 PST 2010

Hi Jan,

Did you try installing from sources? E.g.


  perl cctbx_python_271_bundle.selfx

Just wait a few minutes... done. You'll have the latest of everything.
We don't have the resources to support specific platforms, but it
shouldn't be a limitation since the source installations are extremely

If you need additional Python packages (e.g. numpy) simply unpack
them and run "cctbx.python setup.py" to install them into the Python
you got with the cctbx bundle.

You can also easily use an existing Python installation to build cctbx;
see the docs.


----- Original Message ----
> From: Jan Marten Simons <marten at xtal.rwth-aachen.de>
> To: cctbx mailing list <cctbxbb at phenix-online.org>
> Sent: Mon, December 13, 2010 5:23:09 AM
> Subject: Re: [cctbxbb] How to load a structure from a .cif file?
> Am Samstag 11 Dezember 2010 14:16:37 schrieb Richard Gildea:
> > Hi  Jan,
> > 
> > This should be fairly straightforward:
> > 
> >  from cctbx import xray
> > 
> > xs =  xray.structure.from_cif(file_path="my.cif")
> This looks very good. Sadly I  could not yet test it here, as I'm on gentoo 
> linux and the most recent  version of cctbx there is 2010.03.29.2334 [1]. I've 

> tried to adapt the  ebuild to the most recent release, but as gentoo unbundles 

> boost (by policy  and for good reasons [2]), I'm stuck with outdated patches 
> [3] to the  SConsscripts of cctbx.
> From a gentoo-user pov a simple switch to the build  system to use the bundled 

> or system-wide boost/... would be very helpful  here. That way gentoo 
> developers could easily follow current cctbx releases  without the need to 
> patch all SConscript files. This would help Calculate  linux [4] and other 
> distributions as well, as quite a few base off from  gentoo.
> [1]  http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-libs/cctbx/
> [2]  http://blog.flameeyes.eu/2009/03/23/bundling-libraries-the-curse-of-the-
> ancients
> [3] http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-
> libs/cctbx/files/
> [4] ] http://www.calculate-linux.org/packages/sci-libs/cctbx
> > This will  return you an instance of xray.structure. If you have more than
> > one data  block in your cif, you can specify which structure you want to
> > extract  using the block_heading keyword (by default it just returns the
> > first  structure it can successfully extract from the cif). There is also
> >  similar functionality that can be used to extract miller arrays from fcf  
> > hkl formats.
> > 
> > Please let me know if you have any  further questions about this.
> I was thinking that perhaps a user-driven  wiki for examples and more detailed 

> documentation/howtos might be a nice  addition so that some practical use cases 
> could be documented there. This  might be beneficial for new users of cctbx, as 
> at the moment the  documentation seems to be very much tied to the source code, 
> which is a  rather developer oriented approach.
> With regards,
>   Jan M.  Simons
> Institute of Crystallography
> RWTH  Aachen
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> cctbxbb at phenix-online.org
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