Hi Gunnar,
Using DireX, I am trying to fit a crystal structure into a CryoEM map.
Following your instruction on your web page, I used secondary structure information as restraints.
Alpha helices looks OK, but beta sheets tend to be destroyed.
I don't want to destroy these beta sheets.
To maintain beta-sheet structures, what parameters should I change?
Maintaining beta-sheet structures
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Gunnar Schroeder
- Posts: 9
- Joined: Wed Mar 07, 2007 12:37 pm
RE: Maintaining beta-sheet structures
Hi Takashi,
make sure the den_strength is set to 0.4, den_gamm is zero, and lower the den_secstr_loop parameter carefully from 1.0 to maybe 0.2. In addition, try a weak map_strength (0.01 or 0.02); if the forces from the density map get too large, the structure will deform to much. If this does not help, feel free to send me your parameter file, maybe I find some problematic settings.
Cheers,
Gunnar
make sure the den_strength is set to 0.4, den_gamm is zero, and lower the den_secstr_loop parameter carefully from 1.0 to maybe 0.2. In addition, try a weak map_strength (0.01 or 0.02); if the forces from the density map get too large, the structure will deform to much. If this does not help, feel free to send me your parameter file, maybe I find some problematic settings.
Cheers,
Gunnar