Subject: Re: pipe2ucsf
From: Tom Goddard
Date: Nov 27 3:11 PM

Next: 558

TJ wrote:

Hi--I have sparky and nmrPipe installed in my Mac, which runs OS X
(Tiger), and although Im able to use both programs successfully, I am
unable to use the pipe2ucsf command to convert the nmrPipe output
file to a sparky input file.

I already have Python2.4 installed, so Im not sure what the problem
is. I cannot find pipe2ucsf anywhere in the computer, so Im wondering
what I missed.

Any assistance would be greatly appreciated.

Thanks a lot!

TJ.

Hi TJ,

Yes, pipe2ucsf and the other command-line programs that come with
Sparky are hard to find on the Mac. The are in

Sparky.app/Contents/Resources/bin

You can see inside the Sparky.app folder by right clicking on it and
using menu entry Show Package Contents. But you need to run pipe2ucsf
from a shell. So you should start Terminal on the Mac
(Applications/Utilities/Terminal) and run pipe2ucsf like

/where/sparky/is/Sparky.app/Contents/Resources/bin/pipe2ucsf
file.pipe file.ucsf

See the Sparky manual for details on the pipe2ucsf command syntax:

http://www.cgl.ucsf.edu/home/sparky/manual/files.html#ConvertNMRPipe

By the way, Sparky comes with Python so you do not need to worry about
installing it or having the right version on your Mac.

Tom