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 think

Re: [ccp4bb] pH dependent conformational change

re linked to histidine > residue. Can you point me to any references that show a different pH sensing > mechanism (other than His)? Thanks. > > Best, > Daniel > ------- Mischa Machius, PhD Director, Center for S

Re: [ccp4bb] partial hydrogen refinement.

y at this >>> resolution? 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 >>&g

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 statisti

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

ead 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 Dir

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 experimentall

Re: [ccp4bb] Eleven plausible phasing elements remain unused

hafnium. Since 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

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

some atoms. In such cases, 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

Re: [ccp4bb] generating omit maps

il you actually 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.

Re: [ccp4bb] suggestions for UV spectrometer

. Convenience is one thing... 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

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 On

Re: [ccp4bb] Native Gel Charge States Vs. Conformations Vs. Oligomeric States

- 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 6381 Fax: +1 214 645 6353 On Nov 19, 2008, at 2:56 PM, Jacob Keller

Re: [ccp4bb] Crystallographic computing platform recommendations?

share? Thanks in anticipation of your advice. Regards, Anna Gardberg -------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Da

Re: [ccp4bb] is it Ok to freeze

21-414 5895 University 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 Mac

Re: [ccp4bb] is it Ok to freeze

gy, Oxford 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.;

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

ant enzyme. Also, I would appreciate comments on other possible explanations for this unusual (?) behavior. Thanks a lot Subbu -------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southweste

Re: [ccp4bb] Low resol structure

Andrews is a charity registered in Scotland : No SC013532 -------- 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 21

[ccp4bb] TLS, B factors, phenix and refmac

e contact us for any 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

i-crystal version of RBijvoet The downside of adopting new names is that it makes the previous literature 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

Re: [ccp4bb] ideal bond length and bong angel

grath 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

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

tand- alone coot for OS X 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

[ccp4bb] Coot 0.4 on Mac OS X 10.4

- 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] The importance of USING our validation tools

little or no crystallographic experience. And most important, > a PDB ID should always be released only in combination with such a > summary. > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr.

Re: [ccp4bb] Depositing Raw Data

ith that. Again, just MHO. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mischa Machius Sent: 17 August 2007 15:07 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Depositing Raw Data Since there are several sub-plots in that mammoth threa

[ccp4bb] Depositing Raw Data

ng'. We are happy to share more details of our IT plans with the CCP4BB, such that they can be improved, and look forward to hearing feedback cheers -------- Mischa Machius, PhD Associate Professor UT Southwestern

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] 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 c

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

o share more details of our IT plans 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

[ccp4bb] Mac Pro questions

to share their experience with other graphics cards, or to discuss whether it is worth getting an 8-core machine as opposed to a 4-core. Thanks so much. Best - MM ---- ---- Mischa Machius, PhD Associate Professor

Re: [ccp4bb] off-topic Apple computer question

g 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 D

Re: [ccp4bb] off-topic Apple computer question

ter in the future with a third- party memory chip in it. This strikes me as absolute horse-hockey, but then again, maybe I am not aware of something I should be. Thanks. Bill Mischa Machius, PhD Associate Profe