SIBYLS http://bl1231.als.lbl.gov/ let us be your conduit to structural biology en Copyright 2007 Tue, 23 Oct 2007 11:10:02 -0800 http://www.sixapart.com/movabletype/?v=4.01 http://blogs.law.harvard.edu/tech/rss Review of SAXS combined with crystallography and computation A recent review accepted for publication in Quarterly Reviews in Biophysics by Putnam, Hammel, Hura and Tainer.

]]> http://bl1231.als.lbl.gov/2007/10/review-of-saxs-combined-with-c.php http://bl1231.als.lbl.gov/2007/10/review-of-saxs-combined-with-c.php general announcements Tue, 23 Oct 2007 11:10:02 -0800 The Gel Dilemma Rands is even more obsessed about his writing instruments than Jane and I.

]]> http://bl1231.als.lbl.gov/2007/10/the-gel-dilemma.php http://bl1231.als.lbl.gov/2007/10/the-gel-dilemma.php hardware Thu, 18 Oct 2007 21:08:27 -0800 DOMO's Maiden Voyage Scott Williams, a postdoc in the Tainer group at The Scripps Research Institute, was the first crystallographer to use DOMO. Here he is kicking back and enjoying some of the fine espresso available at the beamline while DOMO mounts his samples from the custom LN2 sample dewar in the hutch.

Scott screened through ~40 samples during his 16 hour shift, and collected several useful datasets.

]]> http://bl1231.als.lbl.gov/2007/10/domos-maiden-voyage.php http://bl1231.als.lbl.gov/2007/10/domos-maiden-voyage.php PX robot Wed, 17 Oct 2007 16:13:05 -0800 The Laptop Herring I would have to say that these sentiments mirror my own when it comes to the appropriateness of laptops in meetings.

]]> http://bl1231.als.lbl.gov/2007/09/the-laptop-herring.php http://bl1231.als.lbl.gov/2007/09/the-laptop-herring.php general announcements Sat, 01 Sep 2007 21:48:24 -0800 Pneumatic Guillotine Lid Installed After determining that operating the LN2 sample dewar without a lid was going to be problematic with regards to ice accumulation in the liquid nitrogen I decided to design and install a pneumatically operated guillotine lid. Here is a nice aerial shot of the closed lid.

hit the jump for details and more pics…

]]> http://bl1231.als.lbl.gov/2007/08/pneumatic-guillotine-lid-insta.php http://bl1231.als.lbl.gov/2007/08/pneumatic-guillotine-lid-insta.php PX robot Fri, 17 Aug 2007 15:52:14 -0800 trust the SIBYLS root SSL certificate I’ve recently (i.e. today) enabled SSL connections to the SIBYLS website. This should give you piece of mind when sending private information across the unpoliced expanse of the internet. Therefore, you can now access bl1231.als.lbl.gov via the following URL:

https://bl1231.als.lbl.gov

The one annoyance of our newly implemented security is that your browser is going to complain every time you try to connect. If this is not annoying to you then read no further. If you’d like a remedy to the situation hit the jump…

]]> http://bl1231.als.lbl.gov/2007/08/adding-ssl-certificate.php http://bl1231.als.lbl.gov/2007/08/adding-ssl-certificate.php general announcements Wed, 08 Aug 2007 12:19:22 -0800 Structure of a Thermus thermophilus 70S ribosome functional complex at 3.7 Å resolution In 2006 the Noller lab from the University of California, Santa Cruz solved the structure of the Thermus thermophilus 70S ribosome at 3.7Å resolution. This work was supported by data collected at both 12.3.1 and has been recently highlighted in the ALS news. The original publication was in CELL.

Korostelev A, Trakhanov S, Laurberg M, and Noller HF, “Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.”
Cell 126, 1–13, September 22, 2006.

]]> http://bl1231.als.lbl.gov/2007/06/structure-of-a-thermus-thermop-1.php http://bl1231.als.lbl.gov/2007/06/structure-of-a-thermus-thermop-1.php Science Highlights Thu, 28 Jun 2007 14:04:09 -0800 Crawl, Walk, Run Today DOMO mounted its first pin from the sample dewar that was filled with liquid nitrogen.

This video is pretty large so unless you are on a fast connection or have alot of time to waste trust me DOMO is finally crawling.

]]> http://bl1231.als.lbl.gov/2007/06/crawl-walk-run.php http://bl1231.als.lbl.gov/2007/06/crawl-walk-run.php PX robot Fri, 15 Jun 2007 22:54:49 -0800 DOMO Lives! After two days of code wrangling, two snapped electrical cables, one crash into the goniometer, and several reconfigurations of the force sensor and gripper arms DOMO is alive. On Friday afternoon DOMO mounted its first sample successfully. There is still much work that needs to be done and many bugs to be ironed out, but the PX robot is now functioning.

]]> http://bl1231.als.lbl.gov/2007/06/domo-lives.php http://bl1231.als.lbl.gov/2007/06/domo-lives.php PX robot Fri, 08 Jun 2007 23:35:19 -0800 Domo Arigato, Mr Roboto The new PX automated sample mounting robot shall henceforth be known as “DOMO” as in Domo Arigato. Mr Roboto.

It’s short and catchy, but isn’t really an acronym for anything… yet

DOMO

Doer Of Mechanized Operations?

or

Dolt whO follows My Orders?

I think beer will be given to the person who comes up with the best acronym for DOMO.

]]> http://bl1231.als.lbl.gov/2007/06/domo-arigato-mr-roboto.php http://bl1231.als.lbl.gov/2007/06/domo-arigato-mr-roboto.php PX robot Thu, 07 Jun 2007 13:41:18 -0800 Sample Dewar take one Being the brave souls that we are we thought we would attempt to make a sample dewar without a lid. Our main concern is ice. We are concerned with the build up of ice around the rim of the dewar, but more important is the prevention of ice accumulating in the liquid nitrogen in the dewar. In order to prevent ice around the rim we have completely covered the top of the dewar with flexable silicon heaters as seen in the following picture.

This design works quite well. We have 240 Watts of heaters being powered by a 48VDC power supply and controlled with a small Minco controller. The prevention of ice building up in the liquid nitrogen is a much more complicated matter. Our present thinking is that a laminar flow of air across the surface of the nitrogen may be enough to draw off any accumulating ice crystals in the air above the nitrogen before they have time to reach “snowflake” size and fall into the liquid nitrogen…. pics and results to follow.

]]> http://bl1231.als.lbl.gov/2007/06/sample-dewar-take-one.php http://bl1231.als.lbl.gov/2007/06/sample-dewar-take-one.php PX robot Mon, 04 Jun 2007 11:03:03 -0800 the Sample Dewar actually fits The Aluminum sample dewar enclosure actually fits. I guess you have to trust the 3D CAD drawings after all.

]]> http://bl1231.als.lbl.gov/2007/06/the-sample-dewar-actually-fits.php http://bl1231.als.lbl.gov/2007/06/the-sample-dewar-actually-fits.php PX robot Mon, 04 Jun 2007 10:55:29 -0800 New Cryojet Mount In order to make room for the new robot sample dewar we’ve reconfigured the xyz stage and mounting hardware for the Oxford Cryojet. As you can see from these two photos the cryojet is now securely fastened to the gold sample stand.

BACK:

FRONT:

This is the contraption that was supporting the cryojet previously:

]]> http://bl1231.als.lbl.gov/2007/03/new-cryojet-mount.php http://bl1231.als.lbl.gov/2007/03/new-cryojet-mount.php hardware Tue, 20 Mar 2007 10:17:32 -0800 Epson arm finally installed! Well it’s finally in. Kurt and I (actually it was mostly Kurt) worked on this most Monday and Tuesday. I had a bit of a freak out when we first bolted the arm onto the bracket. It really looked like it wasn’t going to fit. However, I was greatly relieved when we unfolded the arm and it turned out just as we had designed it in the 3D CAD software.

This is the clearance between the end of the robot arm and the detector gantry:

]]> http://bl1231.als.lbl.gov/2007/02/epson-arm-finally-installed.php http://bl1231.als.lbl.gov/2007/02/epson-arm-finally-installed.php PX robot Wed, 14 Feb 2007 17:44:07 -0800 New CCD_Z motor and gearbox In order to make room for the Epson robot arm we replaced the straight motor/gearbox combo with a 90º gearbox and equivalent motor.

BEFORE:

AFTER:

]]> http://bl1231.als.lbl.gov/2007/02/new-ccd-z-motor-and-gearbox.php http://bl1231.als.lbl.gov/2007/02/new-ccd-z-motor-and-gearbox.php PX robot Wed, 14 Feb 2007 17:35:50 -0800