[Molvis-list] using Protein Workshop on local PDBs

Douglas G. Scofield dgscofie at indiana.edu
Thu Dec 28 12:34:38 EST 2006

Hi All,

If you're like me, you prefer the simplicity and pleasant results you
get from the RCSB PDB Protein Workshop visualization tool, but you're
just a little annoyed that you can't use it to work on local PDB files.
I'm an evolutionary geneticist, working as a post-doc in Mike Lynch's
lab at Indiana University.  I rarely need a molvis tool, and Protein
Workshop has thus far been pretty much perfect for my needs.  So I spent
a little time, and found a way to get Protein Workshop to open local PDB
files on my local computer.

This method is pretty straightforward and works on Windows machines, at
least.  At the suggestion of John Ferguson at Bard College (who
maintains a nice comparison of free molvis tools at
I'm posting this to the list.

I've described the method at


That server may be a little slow at times.

Briefly: After your first use, Protein Workshop normally resides as a
local Java archive on your computer, and subsequent invocations download
a temporary XML-format file that has a .jnlp extension which directs the
Java Web Start launcher on your computer to start your local Protein
Workshop Java archive.  Within the temporary XML file is a hard-coded
URL for the structure description you've asked the PDB website to
examine, and Protein Workshop downloads this structure from the PDB
website as part of its startup.

All you have to do is keep a local copy of this temporary XML file and
replace the remote URL reference with a URL that refers to a local .pdb
file on your computer, as URL syntax allows you to refer to local files.
As long as the local XML file keeps its .jnlp extension, you should just
be able to double-click it (after you've made the edits) to invoke
Protein Workshop on the .pdb file now encoded within the XML file.  You
can find all the details you need to do this at the webpage above.

I now keep separate local copies of the .jnlp file, one for each local
.pdb I'm using.  I double-click the .jnlp file to start working the
structure with Protein Workshop.

The webpage above contains example .jnlp files to get you started.
There's a lot of words to help you get it right, but once you know the
method, it's very very simple to use, hardly more than a cut and paste.

I hope this is helpful!



Douglas G. Scofield, PhD        Department of Biology 
dgscofie at indiana.edu            Indiana University
off: (812) 856-0115             1001 E. 3rd St.
fax: (812) 855-6705             Bloomington, IN  47405-3700
cell 1: (812) 219-5373          cell 2: (786) 514-9141

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