Re: [ccp4bb] [Err] Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more

: 4.0.0 -- Forwarded message -- From: Amit Kumar amit7urmcc...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Cc: Date: Wed, 19 Mar 2014 21:46:13 +0530 Subject: Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more Before putting in the ligand, there is a clear

[ccp4bb] minimum acceptable sigma level for very small ligand and more

Hello, My protein is 26 kDa and the resolution of the data is 1.90 angs. My ligand is 174 Daltons. and it was soaked into the crystal. Ligand is colored and the crystal after soaking takes up intense color. However if we soak more than optimum, the color deepens in intensity but the crystal

Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more

Before putting in the ligand, there is a clear density for three extra atoms at more than 3 sigma in the Fo-Fc map but for other atoms the density appears around those 3 peaks in the 2Fo-Fc map only and not in the Fo-Fc. Thanks for your reply. Amit On Wed, Mar 19, 2014 at 8:57 PM, Sampson,

Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more

Hi, First, there is nothing magical about contouring a map at 1 rms. The standard deviation of the electron density values really has no relationship to the rms of those values, and appears to generally be much smaller. This is discussed quite brilliantly in the recent paper