[phenixbb] Simulated annealing composite omit map

Pavel Afonine pafonine at lbl.gov
Mon Feb 29 11:41:51 PST 2016

Hi Appu,

at such low resolution you need to use as much information as possible, 
such as secondary structure restraints. There is no sufficient 
information in the data alone to preserve secondary structure. It is not 
surprising it deteriorates after SA.
Maps->Composite omit map
with all defaults should be fine in most cases.


On 2/29/16 06:47, Appu kumar wrote:
> Hello All,
> I am trying to make the simulated annealing composite omit map for a 
> protein ligand complex at 4.37A resolution. I think, Simulated 
> annealing is harsh and  rendering the protein distorting a lot as is 
> evident from the helix turning into the some random structure. In 
> order to avoid this protein distortion in protein backbone, do I need 
> to fix some weight or specific parameter or provide reference 
> structure and put harsh weight ? Any advice or suggestions would be 
> much appreciated.
> Appu

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