Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

2012-01-28 Thread Graeme Winter
Hi Jacob, I think a lot of people do use I/sigma :o) However sigma is in some cases poorly defined, and the merging residuals you refer to are calculated only from the I values and are related to I/sigma anyhow... Of course the R values are sometimes also poorly defined for low multiplicity

Re: [ccp4bb] MAD

2012-01-28 Thread Peter Moody
Ian, If you visit Isaac Newton's old home at Woolsthorpe (near here) you will see a conflicting claim for location of the classic prism experiment. You will also find an apple tree in the garden, but that is another story.. Peter PS this is my special ccp4bb email account, it doesn't always

[ccp4bb] protein lost on membrane of centricon!!

2012-01-28 Thread rashmi panigrahi
Hi all, I tried to concentrate my protein using vivaspin 20 10,000 MWCO PES. The protein was in 50mM Hepes pH 7.5, 500mM KCl and 10% glycerol. I lost about 90% of my protein on the membrane of the centricon. Please suggest some way of concentrating this protein. Will concentrating using peg

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

2012-01-28 Thread John R Helliwell
Dear Jacob, As an editor I am always mindful that an article is finally under the authors' names. That said the reader always deserves to know at what diffraction resolution average intensities (cease to) exist. The usual statistical practice to do that is to use a given quantity's (ie in this

Re: [ccp4bb] protein lost on membrane of centricon!!

2012-01-28 Thread Cale Dakwar
Hello Rashmi, How large are your protein monomer units? Are you expecting these units to have formed an oligomer? As a general rule of thumb, you want your protein molecules to be no smaller than 3x the membrane MWCO. Perhaps all you need is to try concentrating with a lower MWCO membrane,

Re: [ccp4bb] protein lost on membrane of centricon!!

2012-01-28 Thread Cale Dakwar
P.S. I haven't personally tried concentrating with PEG 20K but I suppose it could work. On Sat, Jan 28, 2012 at 12:41 PM, Cale Dakwar c.dak...@gmail.com wrote: Hello Rashmi, How large are your protein monomer units? Are you expecting these units to have formed an oligomer? As a general

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

2012-01-28 Thread Horacio Botti
Dear all Perhaps a bit off of theme, just an example about resolution cut-off mean I/sigma(I) = 2 for dmin = 3.35 A (please have a look at the attached pdf) I would trust in I/s(I) = 2 (in this case it worked), but why not to determine what is information after the model has been refined to

Re: [ccp4bb] MAD

2012-01-28 Thread Colin Nave
Good description from Ian complemented by an amusing aside from Peter. One small point. Ian says The answer is that it turns out that the equation ('Kramer-Kronig relationship') governing X-ray scattering is completely analogous to that governing optical dispersion, Analogous implies the