UROX‎ > ‎

FAQ

"Frequently" Asked Questions about UROX



(1) Where do I find the rpms for VTK ? 

  • http://rpm.pbone.net/ : search for 'vtk' for your distribution
  • http://www.creatis.insa-lyon.fr/vtk/
  • for Fedora/Redhat : ftp://ftp.linuxforum.net/pub1/atrpms/{your_distribution} 
                                          http://atrpms.net/dist/{your_distribution}/vtk/

You will need the rpms for: 
- vtk
- vtk-python (aka python-vtk) 
- python-numpy (aka python-numeric, python-scipy, Numeric)
- python-opengl (optional, for nicer graphics -- aka PyOpenGL)

(2) I get the following message: "Problem importing Fortran modules." What should I do ?

It might occur if you are running a 32-bits version on a 64-bits machine. It that case, just download the right file !
Otherwise, this is linked to changes in Numeric/numpy/scipy python packages among linux distributions.
The easiest is to get the Fortran sources (here) corresponding to these modules and compile them with f2py as follows:

cd UROX/src
make sos

This is equivalent to recompiling by hand:

f2py -c xxx.f -m xxx   (where
xxx is chkmap3, fitin, pep -- respectively)

This will create
xxx.so files that you can use instead of those in the distribution.

(3)  I get an <<emft : problem of sampling>> error. What does it mean ?

It could be 2 things (look at the urox.log file): 
[1] - you have more than 500,000 reflections, in which case it overloads the fixed limits in the program. 
Let me know and I will send a fix. This will be automatically fixed in versions > 1.1.3
[2] - ["incompatible cells" warning in the log file]
 your original map EXTENT did not satisfy Ten Eyck's FFT criteria (see Users Manual), for example it was odd.
In this case UROX padded your map with its average and created a d/tmp.ezd file.
Please re-load that d/tmp.ezd map and the problem will disappear. 
This will be automatically fixed in versions > 1.1.3

(4) What map formats are supported ?

URO works only with EZD map format. 
UROX can load EZD but also MRC/CCP4/PIF map formats, using mapman (Gerard Kleywegt) and pif2ezd (James Conway) that come with the distribution and in fact convert . It optionally converts them into a VTK binary format, which is faster to load than EZD.

(5) Does UROX really require Python version >= 2.4 ?

Well, python2.3 should work (provided it includes Tkinter and you install the corresponding vtk-python packages).
In the urox.py file, replace __RPV=2.4 by __RPV=2.3, this should do the trick. 
You might need to compile new fortran modules (see question 2). 

(6) Does it work for both sh and csh ?

UROX should work with both (use the installbin_{urox_version}.sh or .csh). 
URO (no graphics) only works with csh.

(7) Does it do flexible fitting ?

In UROX 1.1.3 and higher, you can set NORMA=1 in the urox.py file to get access to normal modes perturbation of your structure.
It will be fully supported in UROX 2.*

(8) Where does that weird name come from ?

It is a long story... If you find it to be the acronym of something useful, tell us.
It has nothing to do with the following:
- http://www.glorantha.com/hw/fan/cultshort_urox.html
- http://www.thefreedictionary.com/Urox

Comments