Hello,
I am trying to fit a crystal pdb into a cryo-EM density map using DireX. According to the tutorials on the web, I should do refinement and minimization. However, when I tried to do minimization after refinement, DireX informed me of this information "Did not converge! No structure generated!". I want to know the reason.
Thank you!
why it happens?"DId not converge!"
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Gunnar Schroeder
- Posts: 9
- Joined: Wed Mar 07, 2007 12:37 pm
RE: why it happens?"DId not converge!"
Hi,
did you read in the original model with the -pdb option for the minimization run?
If you want to run several consecutive runs, the scheme looks like this:
direx -pdb start.pdb -cur model1.pdb ...
direx -pdb start.pdb -p model1.pdb -cur model2.pdb ...
direx -pdb start.pdb -p model2.pdb -cur model3.pdb ...
Since DireX learns the topology, bond lengths, angles, etc from the structure read with -pdb , there could be problems when you directly read in the direx output, as small errors in the output accumulate.
Hope this helped.
Gunnar
did you read in the original model with the -pdb option for the minimization run?
If you want to run several consecutive runs, the scheme looks like this:
direx -pdb start.pdb -cur model1.pdb ...
direx -pdb start.pdb -p model1.pdb -cur model2.pdb ...
direx -pdb start.pdb -p model2.pdb -cur model3.pdb ...
Since DireX learns the topology, bond lengths, angles, etc from the structure read with -pdb , there could be problems when you directly read in the direx output, as small errors in the output accumulate.
Hope this helped.
Gunnar