biskit-general

[Raik G. <rai...@cr...>]

Hi Özer,

the problem is very simple: the secondary structure as well as the surface 
calculation and the Pymol visualization depend on external programs that you 
need to install first.

oze...@bo... wrote:
> 
> Hello Sir,
> 
> I want to ask you something about the calculation of fraction of a protein's
> surface is contributed by beta sheets. 
> 
> ## add information calculated by external programs
> d = B.PDBDope(m)
> d.addSurfaceRacer()                   # MS, AS, relMS, relAS and curvature
> d.addSecondaryStructure()             # secondary structure from DSSP

This requires a local installation of a little program called surfaceracer. See:
http://biskit.pasteur.fr/install/applications/surfrace/

and also the installation of DSSP:
http://biskit.pasteur.fr/install/applications/dssp

Please follow the links to the installations instructions. If you are sitting on 
a linux or MacOSX system, this should be a rather quick exercise.

> Furthermore ı wanted to calculate center of mass of a protein but ı could not. 
> 
>>>> from numpy import *
>>>> import numpy.random as R
>>>> import numpy as N
>>>> from Biskit.gnuplot import *
>>>> from Biskit import *
>>>> m = PDBModel( '3D4S' )
>>>> m = m.compress( m.maskProtein() )
>>>> diff = m.xyz - m.centerOfMass()
>>>> dist = sqrt( sum( diff**2, axis=1 ) )
>>>> mask = dist < 10.
>>>> m_center = m.compress( mask )
> 
> Everything is OK but when ı write this line 
> 
>>>> pm = Pymoler()
> Adding color_b.py script as a PyMol command
> Adding color_b.pyc script as a PyMol command
> Adding color_b.pyo script as a PyMol command
> Adding rubor.py script as a PyMol command
> Adding rubor.pyc script as a PyMol command
> Adding rubor.pyo script as a PyMol command
> 

This requires a local installation of Pymol (which also has to be in the search 
path): There are pre-compiled packages available for most linux systems. E.g. on 
  ubuntu a simple "sudo apt-get install pymol" should be enough. See:
http://pymol.sourceforge.net/

Note, all we are doing here is a nice visualization. Alternatively, you can also 
save the numbers in the PDB and use a molecular viewer of your own choice (VMD 
is a good one). Example::

 >>> m['temperature_factor'] = dist
 >>> m.writePdb('3d4s_distance.pdb')

will create a PDB file where the B-Factor column contains the distance values.

 >>> m_center.writePdb('3d4s_center.pdb') will create a shorter PDB file only 
containing the atoms within 10 A of the center of mass.

Just open file number one and color it by B-Factor or superpose file number one 
and two with different colors to visualize the result of the cut.

I hope that helps!
Good luck!
Raik

> ı faced with some errors again.
> 
> Traceback (most recent call last):
>   File "<pyshell#11>", line 1, in <module>
>     pm = Pymoler()
>   File "C:\Python25\lib\site-packages\Biskit\Pymoler.py", line 178, in __init__
>     catch_err=1, catch_out=1, **kw )
>   File "C:\Python25\lib\site-packages\Biskit\Executor.py", line 309, in
> __init__
>     self.exe.validate()
>   File "C:\Python25\lib\site-packages\Biskit\ExeConfig.py", line 228, in
> validate
>     raise ExeConfigError, str(why) + ' Check %s!' % self.dat
> ExeConfigError: binary pymol not found. Check
> C:\Python25\lib\site-packages\Biskit\data\defaults\exe_pymol.dat!
> 
> 
> Please help me as soon as possible.
> 
> Best wishes,
> 
> Özer Özcan
> 
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> .
> 

-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________