The ABINIT Users Mailing List ( CLOSED )

["Nuno A. G. Bandeira" <nuno.bandeira@ist.utl.pt>]

Hua Bao wrote:
> Dear abinit-user,
>
> I am trying to use cut3d to convert *_DEN file to some file easy to 
> visualize. I convert it into molekel type file (choose 7) and then 
> download it to windows system. However, the molekel program cannot open 
> the file."Can not open .... with OpenBabel". Is it because the transfer 
> between Linux and Windows?

Molekel has been redeveloped from scratch and since 5.0 it's still not 
been working very well.
The molekel format is probably readable with the old 4.3 version but I 
won't guarantee it. I suspect the cut3d molekel output is obsolete.

In Windows I would recommend using either VICS/VEND or if you're willing 
to install an Xserver (like cygwin/X for example) you can try out XCrysden.

A good idea for developers would be to create an output option for 
Gaussian cubes which is a well established 3D isosurface format within 
the chemistry community and readable by many graphics programs, 
including molekel.

Regards,

--
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student @ IST,Lisbon
--