Re: [ccp4bb] Reading the old literature / truncate / refinement programs

Hi Ian, The initial question was about which procedures to convert intensities to amplitudes are deemed acceptable. I was proposing the Sivia & David (1994) method as an alternative to the French & Wilson (1978) method. You were objecting against this and came up with data simulations which w

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

traints? Again, apologies for the long delay, and for the essay! Cheers -- Ian > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: 06 October 2008 21:17 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Reading the old liter

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

ly for low average intensity (<= 1 sigma). The Bayesian-corrected intensities are not needed in practice for refinement (but may be better for other purposes such as twinning tests) because the likelihood function can handle the uncorrected negative & zero intensities.Cheers-- Ian

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

e better for other purposes such as twinning tests) because the likelihood function can handle the uncorrected negative & zero intensities. Cheers -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Frank von Delft >

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

I mentioned previously phenix.refine tosses your weak data if IMEAN, SIGIMEAN are chosen during refinement. phenix.refine does not automatically remove the data based on sigma (it does it by user's request only). phenix.refine removes only negative or zero values for Iobs (Fobs). That is

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

Hi Pete, just a remark: On 9/25/2008 4:00 PM, Dunten, Pete W. wrote: I mentioned previously phenix.refine tosses your weak data if IMEAN, SIGIMEAN are chosen during refinement. phenix.refine does not automatically remove the data based on sigma (it does it by user's request only). pheni

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

Can one make it? If so, what's the keyword? Because I couldn't it in the online docs. Cheers phx Peter Zwart wrote: phenix.refine also might not (by default) use missing data in map calculation. AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe this changed now). When your h

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

phenix.refine also might not (by default) use missing data in map calculation. AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe this changed now). When your high resolution shells are incomplete (like when using the anisotropy server to perform elliptical data truncation, or etc

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

Another factor may be that phenix.refine does not make a full use of experimental phase information in its calculation of the error parameters - I've been discussing this with Peter, Randy and Ralph. I don't know that this is the cause, but I see inferior results when recycling buccaneer with

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

This goes back to my previous idea about using the Bayesian estimates ( & sig()) of I & sig(I) in the refinement instead of the measured ones. This would remove any objection to using negative observed intensities, though it's hard to see what exactly the objection is. Basically you're just moving

[ccp4bb] Reading the old literature / truncate / refinement programs

I mentioned previously phenix.refine tosses your weak data if IMEAN, SIGIMEAN are chosen during refinement. I'm wondering if this omission of weak Fobs from the Fobs-Fcalc difference map explains why the difference maps out of refmac seem to be more helpful in showing where to move atoms.