Re: [ccp4bb] DANO from PDB

Eleanor Dodson wrote: Well - the old way to estimate sigma was Sqrt(I**2 + constant_representing background) and then get Sigma_F as ~ sqrt(SigI)/(2*F ) . sftools would calculate that for you and append it to the output file.. Eleanor I suggested something similar to Pete but sufficiently diff

Re: [ccp4bb] DANO from PDB

Well - the old way to estimate sigma was Sqrt(I**2 + constant_representing background) and then get Sigma_F as ~ sqrt(SigI)/(2*F ) . sftools would calculate that for you and append it to the output file.. Eleanor Eleanor Peter Adrian Meyer wrote: I add a fake "sigma" column for each "data" col

Re: [ccp4bb] DANO from PDB

Wouldn't it be reasonable to use the sigma one calculates from the sigmaA? That sigma would reflect the uncertainty in the calculated structure factor amplitude due to the uncertainty in the parameters in your model. Of course, one then realizes that you should down weight you structure facto

Re: [ccp4bb] DANO from PDB

> I add a fake "sigma" column for each "data" column because so many programs require one. This is slightly tangential, but does anyone know of a good way to generate semi-realistic sigma values for calculated/simulated data? The best I've been able to do is borrow from an experimental dataset of

Re: [ccp4bb] DANO from PDB

Hi Santosh, Here is an alternative to methods mentioned earlier. If you get the latest version of the cctbx or cci_apps (from www.phenix-online.org) you will find a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). xmanip has some useful features, one of t

Re: [ccp4bb] DANO from PDB

And just to be complete . . . Solve will calculate data with the anomalous component for you, although you can't stop it from adding some "experimental" error. Phenix.refine is another option. Pete

Re: [ccp4bb] DANO from PDB

I wrote a CCP4 script for this: http://bl831.als.lbl.gov/~jamesh/mlfsom/ano_sfall.com The script is actually based on a CCP4BB reply from Elanor I found in the archives. It does Elanor's jigery-hokery, and a few other things. The script is meant to be the front-end for a simulator so I did a

Re: [ccp4bb] DANO from PDB

Dear Santosh, You can do it easily with XPREP, but you need first to convert PDB format into SHELX .ins format using the 'I' option in SHELXPRO (just answer all questions with for this purpose), then start XPREP without an input file and give the name of the .ins file when it prompts for a fi

Re: [ccp4bb] DANO from PDB

Santosh Panjikar wrote: Hi all, Does anybody have a program which can calculate anomalous differences or F+ and F- from a refined structure at given wavelength and resolution ? Thanks Santosh Santosh Panjikar, Ph.D. [EMAIL PROTECTED] Staff Scientist EMBL Hamburg outstation

[ccp4bb] DANO from PDB

Hi all, Does anybody have a program which can calculate anomalous differences or F+ and F- from a refined structure at given wavelength and resolution ? Thanks Santosh Santosh Panjikar, Ph.D. [EMAIL PROTECTED] Staff Scientist EMBL Hamburg outstation http://www.em