[ccp4bb] helix translation

Dear colleagues, I am analyzing a helical segment that looks a bit off from the traditional alpha-helix. Does anyone knows a program for calculating alpha helix translation per residue along the helical axis? Thanks, Young-Tae Young-Tae Lee, Ph. D. Research Associate David Goodin lab Dept

Re: [ccp4bb] LINK option during refinement

] On Behalf Of Garib Murshudov [ga...@ysbl.york.ac.uk] Sent: Thursday, June 24, 2010 4:57 PM To: Young - Tae Lee Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] LINK option during refinement In your run with the option "residues are close only" refmac also should generate a pdb file with

[ccp4bb] LINK option during refinement

Dear Dr. Murshudov, I am working on the heme protein with a surface Cys residue covalenlty linked to another molecule through its SG atom. Here is a part of log file. -- INFO: link is found (not be used) dist= 2.188 ideal_dist= 2.300 ch:AA res: 400 C

Re: [ccp4bb] Calculation of angle between two helix of different subunits

subunit in different orientation. Suggestiona would be appreciated. Thnaks in advance Peter Young-Tae Lee, Ph. D. Research Associate David Goodin lab Dept. of Molecular Biology The Scripps Research Institute

[ccp4bb] Order of scale/merge and reindexing

300 cycles of refmac5 refinement. Then R/Rfree converged to 0.20/0.25. However, I am not sure whether this improvement was really from correcting order of scale/merge and reindex, or still from including previous test data in the new refinement. Thanks, Young-Tae Young-Tae Lee, Ph. D

Re: [ccp4bb] X-Ray versus NMR Structure

*** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: [EMAIL PROTECTED] ************** Young-Tae Lee,

Re: [ccp4bb] asymmetric oligomers

Here is one like that. Chaperoned Ubiquitylation—Crystal Structures of the CHIP U Box E3 Ubiquitin Ligase and a CHIP-Ubc13-Uev1a Complex . Molecular Cell , Volume 20 , Issue 4 , Pages 525 - 538 M . Zhang , M . Windheim , S . Roe , M . Peggie , P . Cohen , C . Prodromou , L . Pearl Young-Ta

Re: [ccp4bb] Puzzling protein-protein interaction

Hi Brett, As Filip pointed out, pulldown assay is not an equilibrium experiment. In addition, one of protein should be attached to the resin in the pulldown assay, which might not be sometimes favorable. You might not want to make very quantitative analysis on the pulldown results. If I