[ccp4bb] Cut ligand or keep in whole piece when only part of it can be resolved

[Jay Pan]

Hi everyone,

I have two types of ligands cocrystallized with my protein, ligand 1 and ligand 
2. I am only interested in resolving ligand 2. In my electron density map, only 
part of ligand 1 can be identified. Is it ok for me to cut ligand 1 so only the 
identifiable part is left or should I keep the whole piece?  Thanks in advance.

Jay

[ccp4bb] Should I be worried about negative electron density?

[Jay Pan]

Hello Everyone,

I have a reasonably well fitted electron density map through molecular 
replacement. However, there is always some red region left no matter how hard I 
tried when the mtz file is loaded into Coot. Is this because my model is still 
not good enough or it’s natural to most model fittings. In another word, should 
I be worried about the red region? Thanks in advance.

Jay 

[ccp4bb] updated mtz file or original one in refmac5

[Jay Pan]

Hello every one,

I am just starting to use refmac to do refinement. There is an mtz output file 
each time. Should I use this one for further refinement or should I use the 
original mtz file (the one after scaling)? Thanks.

Jay