[chimera-dev] Protofibril model

[lihong huang]

Hi Russ, Elaine and Tom,

Thank you very much for your help. We will try what you suggested and let
you know how it works.

Best,
Lihong

On Thu, Jun 9, 2011 at 3:13 PM, Russell M. Taylor II <taylorr at cs.unc.edu>wrote:

> 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<http://www.cs.unc.edu/%7Etaylorr>
> University of North Carolina,                     Voice: (919) 962-1701
> Chapel Hill, NC 27599-3175                        FAX:   (919) 962-1799
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