one hour outage this morning was wobbly or down for three hours this morning after a surprise ("surprise!") test of emergency power went pear shaped. We believe everything is back up and normal now. Please let us know if anything does not seem to be working (more than usual).

-- John

DataWarrior as a very cool molecule dataset analysis tool

DataWarrior is a free cheminformatics program for data visualization and analysis. Kudos to Actelion Pharmaceuticals Ltd for making this amazingly powerful tool available. And did I mention it is free?

Just wow.

1000 apologies - DUDE and DOCK Blaster working again

Dear long-suffering, patient, and most honorable fans

DUDE decoy generation is working again, and DOCK Blaster is better too.

I am sorry I let this problem fester over the last 2 weeks. I promise to make it up to you (dinner and a movie?). But seriously folks, I will now write to everyone who has written me in the last few weeks.

And I promise to be a better hobbit, going forward.

-- John

We are experiencing technical difficulties

Dear fans

We have been experiencing problems of unknown etiology. I don't believe in ghosts, so we're just continuing to proceed in a logical series of steps until we get to the bottom of this. It is taking longer than we expected.

bottom line: please be patient while we figure out what is wrong. Some things work, some don't. Sorry.

-- John power outage

Dear fans

We've got a new hospital going in across the street here in San Francisco and they want to turn the power off twice - this week and next.

We're warning you that, ZINC, DUDE, DOCK Blaster, SEA, DISI and so on may be offline during the night of October 1 and October 9 here in San Francisco. In each case, the cluster should come back to full strength the next morning around 9am local time.

Thank you for your understanding.


User Appreciation Day

Dear Users of DUDE, DOCK Blaster and services generally:

First, we would like to take this opportunity to thank you for your interest in our work and your patience when things go pear shaped.

Second, we've had a series of unfortunate events over the last week that have led to interruptions in the DUDE decoy building service, and, because it uses it to make decoys, DOCK Blaster. As a result, jobs have been mysteriously hanging or dying.

ZINC and the rest of is back up

We were down over the long weekend, beginning Sunday morning through early Monday morning in San Francisco. We are back up now. Thank you for your patience.

download (large) arbitrary subsets based on ZINC ID

People ask "how can i download 100,000 (or more) custom ZINC molecules in say mol2 or SDF format" . Well, there's an old saying that goes, give a person a custom database and they'll dock for a day. Give them a wiki page that describes how to download arbitrary and arbitrarily large subsets in a format of their choosing and they'll dock for a lifetime. In that spirit, I give you you give the script a list of ZINC IDs as test.list. We split them up into chunks of 1000, and download each molecule separately. is up and running

We're just happy to tell you that we have not been down now for a whole day, and things seem to be working much better. Be sure to let us know if you have any trouble at all!

-- John

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