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 http://biology.bard.edu/ferguson/course/bio301/Links_Programs.shtml), I'm posting this to the list. I've described the method at http://intron.bio.indiana.edu/~scofield/local_protein_workshop/ 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! Cheers, Doug 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