Running the Bilateral Filter in Chimera

Runs the bilateral filter found in EMAN's proc3d program on a density map.


1. INPUTS

Required Parameters:
input file Any even, cubic MRC file
NOTE: The input file can be entered through the selection button, which displays all appropriate open models in chimera. Additionally, the user can specify a file not currently open in Chimera by selecting the "use external file" option button and typing the name of the file, in the current working directory, into the entry box.

Bilateral Filter Options
sigma1
filter for distance
sigma2 
filter for value
iteration
number of cylces, typically 1
width
peak width


2. Control Buttons:        

Apply Executes helixhunter with desired inputs and options within Chimera
Close Exits bilateral filter submenu
Help Launch this help window

 
3. Outputs

hh-*.pdb helixhunter output in PDB format


4. FAQ

1. What input will the bilateral fitler accept?
For the input files, the bilaterl filter accepts all volume files read by EMAN (mrc, imagic, etc...) although Chimera only reads MRC files directly.  

2. What is the output of foldhunter?
A MRC file

3. Why is my EM density not scaled and center correctly?
Chimera and EMAN use different conventions for the assigning the origin of a density map.  In the volume viewer, click on the data button in the top of the panel and set the voxel size to ang/pixel value.  Also set the X,Y,Z origin to (-0.5*MapSize)*(voxel size).

4. Is there any major difference between this version of the bilateral filter and the EMAN's proc3d blfilt option?
Nope.

5. Is there a non-graphical version of this new helixhunter?
Yes. proc3d <in> <out> blfilt=sigma1,sigma2,iter,width

6. How long does helixhunter take to run?
The bilateral filter can take as little as a few seconds to long as a few hours.  depending on size and filter options.

7. Why don't the results  look right?
Choose your filter parameters carefully.  This is documented in the paper by Jiang et al.

5. More Help

Help... I still don't get it./I can't read./I can't follow instructions.
You can contact me or check out the EMAN documentation.

http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc

contact information:
Matthew Baker
mbaker@bcm.tmc.edu
713-798-6989