SBGrid Consortium - News and Events

We are proceeding with compilation of a new high-performance computing branch of the SBGrid software. This new branch will include applications optimized for batch and parallel computations for both Linux and OSX grid environments. The distribution will be available to users utilizing the grid through the General User Program (http://sbgrid.org/gup). This month’s Grid General User Proposal awardee is a lab at Yale Medical School for molecular dynamics calculations.

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Some of the software we provide can be tricky to use. That’s why we’re here – to help simplify ease-of-use of this software. In the Software Hints section of our newsletters, we’ll provide a hint or two on selected software.

This month’s hint: Opening an “o” binary file on a newly-licensed computer

You might open an old o binary file on a computer that has been recently licensed, only to find out that all save features are still disabled. All you will need to do is to read the license file after the binary file is open. From your O prompt: read /programs/share/o/access.o

Have a hint to contribute? Please submit your hint to hint4ipod@sbgrid.org. All hints will be included in an iPod drawing scheduled for Dec 31st.

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Dear Consortium Members and Affiliates,

Time to announce our software updates for November. This month’s highlighted updates include CNS version 1.2, HKL2000 696, EMBOSS and 2DX version 2. Updates will begin on Friday and you should be able to use all the new software on Saturday. In this newsletter, we will also welcome our newest members and update you on our support of the latest Fedora Core release. Also read on for your chance to win an iPod shuffle in our Software Hints section.

Kind Regards,
Piotr Sliz
Group Leader
Structural Biology Computing Group, SBGrid

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The following software will be available after this weekend's updates:

CNS 1.2 will be available exclusively to SBGrid members. New improvements include
- updated bulk solvent model and scale factor calculations (developed for robust refinement and low resolution applications)
- new bulk solvent and scaling routines in structure deposition files
- fixed bug when a structure has a lower resolution that the default Wilson limit
- automatic and fixed bulk solvent parameter options

Thank you Axel for providing this distribution to SBGrid members ahead of general public. Since all users are likely to take advantage of new improvements immediately we will make version 1.2 the default version. If you want to keep using version 1.1 instead please execute the command sbgrid -h for more info. The new CNS …

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A number of labs joined SBGrid in the past month. Our new groups include the Yifan Cheng and JJ Miranda labs from UCSF, the Jin, Ealick, Cerione, Ke, Sondermann and Crane groups from Cornell University and the Swairjo laboratory from Western University.

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