Re: [ccp4bb] I/sigmaI of 3.0 rule

Roberto, The reviewer's request is complete nonsense. The problem is how to best and politely respond so as not to prevent the paper from being accepted. Best would be to have educated editors who could simply tell you to ignore that request. Since this issue comes up quite often still, I

Re: [ccp4bb] pH dependent conformational change

that show a different pH sensing mechanism (other than His)? Thanks. Best, Daniel --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer

Re: [ccp4bb] partial hydrogen refinement.

? Can CCP4 even do this? Should we switch to Shelx or Phenix? It is important to find out what the oxidation state is for the ligand at the pH we crystallized the protein and complex. thanks --- Mischa Machius, PhD

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

Lake Wobegon!!! For those outside the US and/or otherwise not familiar with that small town, check out: http://en.wikipedia.org/wiki/Lake_Wobegon Lake Wobegon, where all the women are strong, all the men are good looking, and all the children are above average The best use of modern

Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries

look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm --- Mischa Machius, PhD

Re: [ccp4bb] degradation of protein durring freez thaw

A couple more thoughts: 1. thermodynamics says that proteins denature at low temperatures just as they do at high temperatures. 2. flash-cooling does away with some of what thermodynamics says (not an equilibrium process anymore) 3. Whether a given protein can be frozen needs to be

Re: [ccp4bb] Eleven plausible phasing elements remain unused

these were not successful I should probably write them up and publish in the Journal of Failed Crystallization Experiments. Cheers - MM Mischa Machius, PhD Associate Professor Department of Biochemistry UT

Re: [ccp4bb] two identical proteins in one asymmetric unit

, I think this area has not received proper attention yet. But it should, because I have the feeling that the impact of a great set of tools would be immense. Eternally hopeful - MM Mischa Machius, PhD Associate

Re: [ccp4bb] generating omit maps

, I use a mixed strategy derived from the approaches described in my first post. Best - MM On 10 Dec 2008, at 16:41, Mischa Machius wrote: Kathleen - The easiest way is to simply remove the ligand from the coordinates and refine for a few cycles. Whether that is particularly meaningful

Re: [ccp4bb] generating omit maps

include the ligand). Best - MM Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645

Re: [ccp4bb] suggestions for UV spectrometer

Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

Re: [ccp4bb] Crystallographic computing platform recommendations?

Gardberg Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645

Re: [ccp4bb] is it Ok to freeze

University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A

Re: [ccp4bb] is it Ok to freeze

of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/ klaus/ - On 19 Jun 2008, at 18:04, Mischa Machius wrote: Ha, everyone

Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle

appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas

[ccp4bb] TLS, B factors, phenix and refmac

details. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

Re: [ccp4bb] differences between Rsym and Rmerge

obsolete, but I wonder if the older terms were ambiguous enough that that's not such a problem. -- Christopher Putnam, Ph.D. Assistant Investigator Ludwig Institute For Cancer Research Mischa Machius, PhD Associate

Re: [ccp4bb] ideal bond length and bong angel

wrote: Bong angels are probably ideal already! Please explain, so that I can teach this to my students. :) Jim Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines

[ccp4bb] Coot 0.4 on Mac OS X 10.4

Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

Re: [ccp4bb] Coot 0.4 on Mac OS X 10.4

10.5 intel. http://tinyurl.com/24mchk It might work on 10.4 intel as well. I have not tried it. Everything you need is sequestered in /usr/local/coot Peace and Joy, Bill Mischa Machius wrote: Y'all - I was wondering if anyone had a precompiled, stand-alone binary (Universal or Intel

[ccp4bb] Depositing Raw Data

with the CCP4BB, such that they can be improved, and look forward to hearing feedback cheers Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390

Re: [ccp4bb] The importance of USING our validation tools

with the CCP4BB, such that they can be improved, and look forward to hearing feedback cheers Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX

Re: [ccp4bb] The importance of USING our validation tools

Hmm - I think I miscalculated, by a factor of 100 even!... need more coffee. In any case, I still think it would be doable. Best - MM On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote: I don't think archiving images would be that expensive. For one, I have found that most formats can

Re: [ccp4bb] The importance of USING our validation tools

Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

Re: [ccp4bb] off-topic Apple computer question

, but then again, maybe I am not aware of something I should be. Thanks. Bill Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A

Re: [ccp4bb] off-topic Apple computer question

the repair. I just inquired: it's a flat rate of $329 in all cases, except when the LCD panel needs to be replaced. Cheers - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323