Continue reading »]]> New package!

Platon has a very fast releases which make things difficult to keep the package up to date. There is now an automatic build (build at 3am GMT+1) of platon for fedora 13,14 and 15 and for centos 5 and 6. The build on centos 6 is broken at the moment though.

The package name is platon-nightly in debroglie-nightly repository and does not interfere with the platon rpm. The usual platon rpm will remain.

To activate the new repository, you need to update debroglie-release. It will also update the repo link to the new server.

Debroglie repository

Continue reading »]]> After a recent test of Olex2-GUI rpm it became clear that the update mechanism I had used was not working correctly causing new installs to appear broken. This was exacerbated by a path typo in the Olex2 startup script installed from the Olex2-binaries.

I have now fixed both issues and moved the usettings.dat file to the GUI.

The current olex2-gui is pulled from the branch/1.1 svn and updated from a working version. It also includes all of the script codes which with the appropriate entries in the usettings.dat and modification of etc/scripts/customScripts.py to read:
#import example
import batch_overlay
import OlexSir
import OlexPlaton
import OlexMail
import OlexCheckCIF
import OlexCDS

(This will be made default in the next update).
Will activate these following commands:
spy.OlexCDS()
spy.OlexMail()
spy.OlexPlaton()
spy.OlexSir()
spy.OlexCheckCIF()
spy.flipsmall()

This update however does break the sync between olex2 and the repo we are neither a tag nor their beta or alpha release. Because of this I have disabled the internal olex2 userspace update mechanism updates will come via the GUI.rpm for now until they catch up with us.

Continue reading »]]> New rpms for CCTBX, Olex2 and Olex2-GUI have been uploaded to the testing repo (only takes 7 hours to do this) only to find that the CCTBX had a bug so yet another CCTBX was uploaded yesterday (6 hours) to resolve it.

All Centos 5 build was using the Epel 5 extras python 2.6 environment (Centos 6 via native 2.7).

The new CCTBX and Olex2 binaries bring us pretty close to the official 1.1.4 release which is imminent but for the GUI. The GUI is proving to be contentious so I am planning on changing how the GUI rpm is created and how it updates the user space (wish me luck on this). As it stands Olex2 will work but the native refinement package in the 1.1.4 bins and CCTBX is too advanced for the GUI (go figure) it is a rather big mess!

On the bright side there is a new version of Platon in the release area.

J
(and yes I have been very rubbish at posting news updates here – mainly because I do not want to move Pascal’s lovely posts down the list – how nice are they?)

Continue reading »]]> Fedora 14 is out! Get Fedora

The repisotory for fedora 14 is open. I just put the following packages:

• 2010-11-09: objcryst-fox-1.9.0.2-1.R1269.fc14
• 2010-11-09: objcryst-fox-debuginfo-1.9.0.2-1.R1269.fc14
• 2010-11-09: debroglie-release-14-1.fc14
• 2010-11-09: newmat-11-2.fc14
• 2010-11-09: newmat-debuginfo-11-2.fc14
• 2010-11-09: newmat-devel-11-2.fc14
• 2010-11-09: flipsmall-20090610-2.fc14
• 2010-11-09: EDMA-20090927-2.fc14
• 2010-11-09: platon-101108-1.fc14
• 2010-11-08: superflip-20100920-1.fc14
• 2010-11-08: superflip-debuginfo-20100920-1.fc14

superflip, platon and objcryst-fox have been updated compared to the version in the other repositories.

Continue reading »]]> Edit: all calculations on non-centrosymmetric structures are wrong. I am working on a solution.
Edit 11/10/2010: Fixed in 0.3 version available on the repo.

Two new packages made it in the fedora repos. Not in centos, I used featured in fortran and python not available in the versions of gfortran and subprocess

edensgrid calculates (difference) electron density grids. The input is a list 3 fcf file from shelx, the output, an ascii file with the 3D array flattened (2D slices separated by two blank lines). The fourier transform is done with fftw3.

ediffana calculates some stats and plot the distribution of the difference electron density maps (like in wingx). As this is the difference between the model and experimental data, the result should be a normal distribution. Otherwise, you are missing something in your model. The input is a cif file and a electron density map from edensgrid. The ouput is a gnuplot graph or a matplotlib output (default) with some stats in the terminal.

To launch ediffana, just type “ediffana” and your filename without extension, you can put multiple filenames and the graphs will be stacked in one window.

To install them, just yum ediffana and/or edensgrid
For the usage, in a terminal, just type ediffana ‐‐help or edensgrid ‐‐help, the are a few more options.

Source files are here:
https://redmine.debroglie.net/attachments/download/6/edensgrid-0.1.tar.gz
https://redmine.debroglie.net/attachments/download/3/ediffdensity-0.1.tar.gz


#### m104i ####
mean: -0.0000
median: 0.0029
s^2: 0.0657
min: -0.3155
max: 0.6505
Skewness: -0.013 (normal: 0)
Kurtosis: 1.440 (normal: 0)
Normal test: 2.72e+04, 0.00
Report of linear regression of the normal probability plot:
Slope = 0.9948, Intercept = -0.0000
r2 = 0.990
partial fit (left side):
Slope = 1.3925, Intercept = 0.0480
r2 = 0.985
partial fit (right side):
Slope = 2.2717, Intercept = -0.1862
r2 = 0.950


If there is any problem, feel free to talk about it in a comment or send me an email to pascal22p@parois.net. These are not heavily tested yet.