Running Helixhunter in Chimera

Helixhunter identifies alpha helices in an input density map.  Ouput results are now given in several formats, including PDB and text files.  A bilateral filter option has also been included.

1. INPUTS


Required Parameters:
input file Any even, cubic MRC file
apix Angstroms/pixel
da angular search step, default=5
percen correlation value at which helices are generated
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.

Optional Parameters:
Normalize Normalizes input map using proc3d option, deafult=disabled
Correlation
Runs cross correlation function prior to segmentation, helix identification and display, deafult=disabled
Bilateral Filter Pre-processing input map using the bilteral filter option in proc3d, default=disabled
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 helixhunter submenu
Help Launch this help window

 
3. Outputs


hh-*.iv helixhunter output in inventor format
hh-*.pdb helixhunter output in PDB format
hh-*.sse
helixhunter output in DejaVu format
int-*.txt intermediate results from correlation step (*-coeff.mrc contains raw correlation values)


4. FAQ

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

2. What is the output of foldhunter?
Foldhunter will produce an inventor, a PDB and a DejaVu text file.  If the correlation option is used, three MRC files are generated.

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 helixhunter and the EMAN helixhunter2?
Not really.  The Chimera version of foldhunter uses helixhunter2 and wraps it with some additional control logic and new options like filtering and PDB output.

5. Is there a non-graphical version of this new helixhunter?

Yes. EMAN is now distributed with helixhunter.py which mimics much of the behavior found in the Chimera version of foldhunter.

6. How long does helixhunter take to run?
Helixhunter can take as little as a few seconds to long as a few hours.  With the correlation step enable, typical size density maps will require 5-10 minutes to identifiy helices.  Without this option enabled, helix identification should take less than 10 seconds.

7. Why doesn't helixhunter look right?

Helixhunter attempts to identify helices at a given threshold (percen option).  It may require some manipulation of this value to get the best set of helices.  Good values are generally between 0.4 and 0.2 when using the correaltion option and around 0.8 - 0.9 without the correlation option.  Also, manual tweaking of the helices may be required (use helix module)

8. Are there any statistics to judge the qualtiy of of a helix in helixhunter?
Sort of.  Each helix is given a correlation value.  This value is relative only to the the given input file however.

5. Examples

1. Find helices in a density map quickly.
Open chimera and read in the files of interest. Under Tools, EMAN open helixhunter  Select the MRC file as the target. Enter Ang/pix and percen in the required options.  Push "Apply". Wait for helixhunter to finish execution.  A PDB representation of helices will appear.  Repeat as necessary. Enjoy.

2. Find helices in a density map using the correlation routine. (slow)

Open chimera and read in the files of interest. Under Tools, EMAN open helixhunter  Select the MRC file as the target. Enable the correlation option.  Enter Ang/pix and percen in the required options.  Push "Apply". Wait for helixhunter to finish execution.  A PDB representation of helices will appear.  If the helices do not appear correct, read in the correlation file (int-*-coeff.mrc). Disable the correlation option.  Enter a new value for percen. Push "Apply". Wait for helixhunter to finish execution.  A PDB representation of helices will appear.  Change percen value as necessary and repeat. Enjoy.

6. 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 foldhunter/helixhunter webpage and EMAN documentation.

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

contact information:

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