RCSB PDB Webinar follow-up post: further questions?

The February 15th “How to use the RCSB Protein Data Bank” webinar may generate some questions that we won’t have time to cover or there may be further questions that arise. So we’ll leave this blog post open for follow-up on issues that arise from our discussion. Feel free to add your questions as comments to the post.

The slides from that webinar are available here:

RCSB PDB tutorial and training materials

If you didn’t have a chance to fill out the survey, here’s the link: http://www.surveymonkey.com/s/3WZSR98

Questions from the webinar chat:

1.  We were asked about differences in what I was showing in my screenshots, and what people were seeing on RCSB PDB pages. There are two possible reasons that this might be.

The first reason is that not all structures are associated with all types of information. For example, if you compare the 2ara structure summary page to the 2arc structure summary page you will notice that the 2ara page is the apo form of the molecule and does not have a ligand, a “Ligand Chemical Component” area, or an area for External Ligand Annotation information. The 2arc structure is bound to its ligand, alpha-L-arabinose (or ARA) and so it does have both Ligand Chemical Component area and an area for External Ligand Annotation on its page. The information that you see on various RCSB PDB pages will depend on what is available for the specific entry that you are looking at.

The second reason is a bit more trivial, but equally important – RCSB PDB pages are constantly being updated, and so while the screenshots in our training materials do accurately represent the overall organization and features of resource pages, specific numbers, reference lists, etc. may change over time from what our screenshots show. We work closely with the RCSB PDB developers to keep our materials up-to-date with major software updates that would dramatically change functionality of the tools we present.

2. Another great set of questions that we got during the webinar is whether people could use our materials for their students, and where to download our free training materials on the RCSB PDB.

We would be delighted if our materials were used to teach students, or were presented as a group meeting, etc – really any non-profit use of our freely available materials is fine by us – as long as you don’t remove our copyright notices. We often “train the trainer” in our live seminars or webinars, who then go out and further the reach of our materials by using them to train others at their institutions. And we’ve heard that our materials are great to use in a classroom because not only do we offer the online modular tutorial movie that can be watched online from any browser, we also provide PowerPoint slides with the full script text, handouts for note taking, and an exercise document that can be handed out as a class assignment, or used for a classroom “walk through” discussion.

All that leads to the next part of the question, where can I download OpenHelix’s free training materials on the RCSB PDB? You can download materials free of charge, and without registering at our RCSB PDB tutorial landing page. Just click any of the buttons on the page to 1) launch the movie, 2) download any of our materials, or 3) visit the RCSB PDB resource.