[chimera-dev] Protofibril model

[Russell M. Taylor II]

Dear Lihong,
         I am glad to hear that Chimera let you start down this path.
         I'm CCing the Chimera developer mailing list in case they 
know of a better solution.
         You can also join the chimera users list at 
http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users/index.html 
and then post a query there.

The following is a somewhat convoluted path to get where you want to 
go.  Hopefully someone on one of the above mailing lists will know a 
better one.  If you need to go down this path, we should probably set 
a time for us to sit down together and go through this.

         Download MGLTools from 
http://mgltools.scripps.edu/downloads.  I ran the Windows installer.
         This launched the Python Molecule Viewer.
         Select Compute/Coarse Molecular Surface.  Kept the default 
parameters.  This produced a surface that was near the outside of the molecule.
         Clicked to turn off the red dot under the CPK label so that 
we only see the surface.
         Selected File/Save/VRML 2.0 (.wrl) file.  Also saved STL file.

         I was able to load the resulting .wrl file back into 
Chimera.  This should provide you with a simplified model.  You 
should be able to adjust the parameters for the coarse saving to get 
different model quality.

         I attach the resulting coarse model (inside a Zip file) to this email.
         Russ

[Things below I tried that didn't work]

(Fine surface)
         Select File/Read Molecule.  Opened 1EI3.pdb (when I used 
1M1J.pdb, it crashed trying to make the surface).
         Compute/Molecular Surface/Compute Molecular Surface.  Used 
the default parameters (other parameters caused it to crash).  This 
produced a fine molecular surface.  This could be used directly or simplified.

VMD uses a program called MSMS, but can't run it.  When I go to the 
MSMS home page, it eventually redirects me to MGLTools from Scripps.

NOPE:

         You can load the PDB file into the VMD program (File/New, 
select the file name and click Load on the Molecule File 
Browser).  Then select Graphics/Representations from the VMD Main 
menu. Then pull down Drawing Method and select Surf.  Turn off the 
"Apply Changes Automatically" control and then set the Probe Radius 
to 4.0 and click Apply.
         To turn off the little axes display, select Display/Axes/Off
         To save the resulting geometry, select File/Render from the 
main menu.  Pull down "Render using" and select Wavefront.  Change 
the .obj file name to one that is useful to you (I named id 
protofibril.obj).  Click the "Start Rendering" button.

         Open Blender (available from blender.org).  Press delete to 
get rid of the cube that is created by default.
         Select File/Import/Wavefront to load the model.  Pick the 
file name and then click "Import a Wavefront OBJ"

At 10:18 AM 6/7/2011, lihong huang wrote:
>Dear Dr. Taylor,
>
>I am postdoc working in Dr. Susan Lord's lab. According to your 
>suggestion, we set up the protofibril model using UCSF Chimera 
>program which is very nice. Now we want to move on to make small 
>fiber model, however, the program run very slowly when we add more 
>fibrinogen molecules. We are thinking if we could make the 
>fibrinogen molecule lose more details, maybe the program could run 
>easily. Do you know which program could do this? We just want to 
>show the basic shape of fibrinogen, no needs to show very detailed 
>part, such as alpha, beta and gamma chains. Thanks a lot for your help.
>
>Lihong Huang,
>Postdco
>Pathology and lab medicine

---
Russell M. Taylor II, Ph.D.                           taylorr at cs.unc.edu
CB #3175, Sitterson Hall                        www.cs.unc.edu/~taylorr
University of North Carolina,                     Voice: (919) 962-1701
Chapel Hill, NC 27599-3175                        FAX:   (919) 962-1799 
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