docking.org user support (ZINC, DUD, DOCK Blaster) is going on vacation, August 2-10. During this time we simply won't be able to help you, since our Yurt on the Mongolian Steppes had a server crash last week. ;-)
Also, all docking.org services will be off-line 11-noon today for upgrades and maintenance. Everything should be back to normal by noon.
A new production release, version 1.2540, is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production
Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html. For the time-challenged, here are just a few of the reasons you may want to use the new version:
1) new fetch types:
- comparative models from ModBase
- protein pocket data from CASTp database
- small molecule structures from Pub3D
The following subsets are ready for download:
* 3 (drug like)
* 6 (all purchasable)
* 10 (everything - includes things like pubchem)
I have exported them as mol2 and NOT as SDF, since the files are just so darn huge. It is easy to convert mol2 to SDF, using CDK, OEChem/convert.py, OpenBabel, and many other tools.
As always, do let us know if anything is not right, and thanks for your patience. If enough people complain about lack of SDF, I'll do something about it.
Thanks for your patience.
We had a server outage from 2:10 - 4:30 pm local time today. Full normal service was restored at 4:55pm San Francisco time. During this outage, some kinds of ZINC and DOCK Blaster jobs may have failed mysteriously. If you suspect this has happened to you, simply resubmit the job, please.
Subset #10 ("everything") is now available for download. Previously, some of the files were not available.
Subset #6 ("all purchasable") and subset #3 ("drug like") are _still_ in progress. We promise they will be _completely_ finished Wednesday. Thanks for your patience.
We fixed a problem this morning that was causing downloads of ad hoc subsets of mol2, sdf, and smiles files to either a) run forever or b) suddenly abort after 1-3 minutes. We have just tested on a dozen cases, and it now seems to run reliably quickly - taking up to but no longer than about one minute to assemble and download.
Please let us know if you continue to see this problem.
This is 10 days' advance notice that docking.org will be off-line for maintenance Sat 12 July, 2008. Any job or process running at that time will be unceremoniously canceled. The exact time and duration will be announced later. It will be more than 1 hour and less than 24 hrs.
Ever wanted a few molecules at random to test some hair-brained scheme - I mean - breakthrough new theory? Well, now you can get molecules at random, using the new Random Molecules tool from BCIRC, the Bioinformatics and Chemical Informatics Research Center. Just browse to http://bcirc.docking.org/ and pick "Random Molecules" from the "Tools" pull down menu. Or just go straight to http://bcirc.docking.org/random.shtml
The default is to pick 10 molecules, but you can choose any number from 1-100.
The model systems L99A, L99A/M102Q, CCP W191G and AmpC that figure in publications from this lab and are used by other investigators are now available in ZINC.
Go to http://zinc.docking.org/, and choose "Not for sale vendors" from the "Subsets" pull-down menu.
These are beta versions, and are thus subject to change as we find and fix errors.
We have noticed a lot of new searches on our server since ZINC 8 was released. This is good. However, some queries are running very long. To benefit the most people, we have decided to simply terminate long running queries.
If you have a query that is terminated, and you think it should not have been, please write us at support at docking.org telling us what you want, and we will try to figure out a way that is fast and efficient.