Continue reading »]]> Transformers is a python script which can apply symmetry operations or linear maps on crystallographic parameters (coordinates, ADPs, eigenvalues and their esds). It uses the full variance/covariance matrix so the standard uncertainties is correctly calculated.

The calculation is exact, meaning that if you re-refine the structure in the transformed basis, you’ll get the same esds.

I used it to expand some structures to P1 for normal coordinate analysis with NKA. It can be very useful to transpose data between different models.

Source file

Dependencies:
numpy (http://numpy.scipy.org/)
CifFile (http://pycifrw.berlios.de/)
optparse
scipy (http://www.scipy.org/)

help (very basic)
transformers.py –help

Continue reading »]]> I wrote a small script that plot a few graphs from fcf files:
Anafcfweb

The script is in alpha stage with some improvements needed. I do not store the fcf/cif file on the server. However, the eps/png/pdf generated files are stored in a temp folder not publicly accessible.

It’s written in pure php. The original script was in python but I ported it to php because of the poor perfomance of the cgi interface on Debroglie. I also have an opcode cache for php, so it’s much faster.

About the html part, the graphs are rendered with flot. Flot is a plotting library using canvas. I tweaked it a little bit so it gives better performance with the thousands of data points that requires the graphs. Canvas is part of HTML 5 so do not expect any support in Internet explorer. The script is using a compatibility layer called excanvas for IE but it is extremely slow…

Everything is not rendered in canvas, so export of the graph is not possible directly. For this purpose I am generating a picture from the server with gnuplot. There is also a CSV export of the coordinates.

The graphs are interactive, you can peak a reflection to show all the variables, modify the weights and filter the reflections.

Almost everything is done via javascript and the script heavily depends on jquery.

The sources are here : Anafcfweb svn.

Example with the normal probability plot

Continue reading »]]> I am looking around if a planet gathering rss feeds about crystallography or chemistry can be interesting. However, by looking at the websites of the software distributed here, none proposed rss feeds.

So, in the hypothesis I’ll set up a planet. Which feeds can I used? If you know any feeds that can be interesting, post it in a comment. If there is enough material, I’ll think about it.

PS: for those you don’t know what a planet is: in online media, Planet is a feed aggregator application designed to collect posts from the weblogs of members of an Internet community and display them on a single page. Here is an example: http://planet.fedoraproject.org/.

Continue reading »]]> Today we will be updating for you kind and caring Linux people:
Release:

Platon

Version 250909:
- New ALERTS _314 & _908
- Minor Update (Refinement of ALERT_390 & 391)
Testing:
CCTBX
- Nightly build from the 24/09/09 to fix compatibility with Olex2

Then when my ADSL modem has stopped smoking and cooled off I may think about a new test-build of Olex2.

Also after talking with one of the Olex2 guys they are trying to stabilise their build process. Sticking to a more formal alpha/beta release. It would appear that they have released a Olex2 1.1 TAG which I suspect is the equivalent of our 1.0.3+ TAG in the test-repo. So the next release will be in the test repo as Olex2 1.1.0 and I will look to update the release repo with a 1.1 version in due course. To accommodate the alpha, beta stable builds I think I may adopt the gstreamer naming conventions good, bad and ugly but perhaps just have ugly = alpha, bad = beta and good = stable? Feedback would be appreciated. We are also likely to drop the svnTAG off the “good” release as well and no doubt require epoch increments to do so. Sorry!

Continue reading »]]> At some point next week there will be a new Olex2 rpm uploaded to the test-repo. It will now require the CCTBX rpm as a dependency and will be built from the trunk svn rather than tag svn. It will also utilise the new olex2 updating system for the GUI. Let me know how it goes and remember to give feedback.