P212121

We have a page dedicated to tools used in macromolecular crystallography.

My goal is to provide one location that houses a collection of beneficial tools. Having these programs in one spot will ultimately save everyone a lot of time because it would eliminate endless searching. For a long time, ExPASy has been a great site for tools. Unfortunately, it does not appear to be maintained any longer; many of the links are now broken. ExPASy tended to be repetitive and had a lot of tools that we do not need, like Popitam for mass spectrometry.

I have been updating the Tools page with new content but feel that a number of great programs and online tools are still missing.

What are we missing? Should data processing and refinement programs be included (ie. ccp4, cns)? What tools have you been using that are not listed? Could the ‘Tools’ page layout be improved? We need one great location for crystallography tools, can you help?

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• A Web Interface for PDB Databases
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3 Awesome Insights so far | Have Your Say!

1. 

   Paul
   October 27th, 2009 at 4:15 PM #

   Hi Sean – Rather than have a long list of links, you could perhaps arrange them in a a series of dynamic cascading drop-downs. For example, in the first drop-down you could select “structure prediction”; this would then update the next drop-down where you could select “threading”; and a final drop-down would have a list of links to threading sites. It might make it easier to navigate. E-mail me if you need help with the code.

   P.S: It’s not on your list, but one of my favorite web sites to use before embarking on a novel structure determination project is XtalPred. Also, I know you mentioned ExPASy, but the ScanProsite tool they have is really good for primary structure data mining. Finally, there are a number of ligand databases I use, but I think HIC-Up is probably the most important for crystallographers (though PDBeChem is better for newbies).

2. 

   Sean
   October 28th, 2009 at 11:43 AM #

   Thanks for the suggestion about cascading drop downs and offer to help code.

   I have actually been working on putting together a list of ligand databases

   Expasy is good site and has a number of great tools, but think it can be done better especially by making it more relevant to macromolecular crystallography.

3. 

   Sean
   November 10th, 2009 at 9:12 PM #

   Hey Paul,

   I just wanted to give you an update and let you know that I am still putting together a list of crystallography programs. I will drop you a line when I get a most of them together.

   Thanks again.