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

Hi Jan, Did you try installing from sources? E.g. wget http://cci.lbl.gov/cctbx_build/results/2010_12_13_0000/cctbx_python_271_bund... 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 simple. 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. Ralf ----- Original Message ----

From: Jan Marten Simons To: cctbx mailing list 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boost (by policy and for good reasons [2]), I'm stuck with outdated patches [3] to the SConsscripts of cctbx.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 or 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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb