[PyMOL] apbs and pymol in fink (OS X)

[William S. <wg...@ch...>]

> I have the same problem on a mac G5 dual processor with newly  
> compiled pymol
> 0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
> mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
>
> Interestingly, the programs work fine together on my mac G4 laptop,  
> with
> single processor apbs 3.2 but an older version of the mac/x11  
> hybrid pymol,
> using the same pdb files.

Hi Evan:

Could you go into a little more detail about what is going wrong?   
These compile ok for me on both the G4 and G5. I can also take one  
compiled on my G4 and run it on my G5.  Are you running from a  
directory in which you have write permissions?

FWIW there are now fink packages for both X-11 based pymol and for  
apbs (both vanilla and mpi) in fink.  If anyone experiences problems  
with the apbs packages, please let me know, and I will try to fix  
it.  Jack Howarth put together the pymol package, and it permits apbs  
to be used in the plug-in mode.  By default it runs with an x-windows  
based tkinter and display, but you can make an inverse-hybrid that  
uses an X-windows based display and the aqua tkinter in 10.4.x by  
substituting the line /usr/bin/python for /sw/bin/python in the /sw/ 
bin/pymol shell script.

Thanks,

Bill





William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA