From: Cojocaru,Vlad (
Date: Sun Apr 13 2008 - 14:50:44 CDT

Hi Alex,

Thanks for replying !!

I had openSuse 10.0 and upgraded to the new 10.3 (on Athlon 64, 3500+)... I have just seen that all the checkout files were executables on my machine after checkout with cvs following exactly the recipe on the VMD web site ... I cannot explain why all files were executables if by default the permissions are preserved ...

Regarding my second question, I think you misunderstood ... I first downloaded the binaries for vmd-1.8.7a19 ... And with these binaries I had the python problem ... After seeing the problem (and having the problem so many times before with vmd versions earlier than 1.8.6) I thought that the simple solution is just to compile vmd and as I did it before I should be able to do it again ... And that's when I downloaded the code from CVS

I did not do the compilation yet ...

bets wishes

-----Original Message-----
From: Axel Kohlmeyer []
Sent: Sun 4/13/2008 7:58 PM
To: Cojocaru,Vlad
Subject: Re: vmd-l: compilation with python 2.5 and file permissions from the CVS repository
On Sun, 13 Apr 2008, Cojocaru,Vlad wrote:

VC> Dear John, vmd users,

dear vlad,

VC> When I downloaded the latest vmd source from the cvs repository, all
VC> the files were made executable. Is there a way to tell cvs to
VC> preserve file permissions as they are on the vmd cvs repository?

what OS/filesystem are you operating on? with cvs checkout the file
permissions are preserved by default unless the OS does not support it.

VC> And, another question .. Are there any test versions of VMD 1.8.7
VC> compiled with python 2.5 ? I upgraded my OS (I have now python 2.5,

the cvs _requires_ python 2.5. you have to make some (minor)
modifications to the cvs code to compile with older python

VC> tcl is still 8.4.XX) and now I have the same old problem with the
VC> python interpreter in vmd-1.8.7-alpha19 version for LINUXAMD64
VC> (sample error below). Numeric 24.2 is properly installed, tkinter as
VC> well (import site, import _tkinter, import Tkinter, import Numeric,
VC> import numpy work fine in a python window separate from VMD)....
VC> .....That's why I started compiling the latest source code from CVS

so what are your configure options?

VC> Best wishes
VC> vlad
VC> vmd > gopython
VC> Info) Starting Python...
VC> 'import site' failed; use -v for traceback
VC> Traceback (most recent call last):
VC> File "<string>", line 1, in <module>
VC> ValueError: vmdnumpy module not available.

looks like you didn't configure VMD to compile with
numpy support or it didn't link/install properly.

VC> Info) Text interpreter now Python
VC> Traceback (most recent call last):
VC> File "<string>", line 1, in <module>
VC> File "/usr/lib64/python2.5/lib-tk/", line 38, in <module>
VC> import _tkinter # If this fails your Python may not be configured for Tk
VC> ImportError: No module named _tkinter
VC> >>> import _tkinter
VC> Traceback (most recent call last):
VC> File "VMD", line 1, in <module>
VC> ImportError: No module named _tkinter

i just updated/recompiled on my machine and it is working fine for me.



Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.