[Chimera-users] [chimera-dev] Protofibril model

Tom Goddard goddard at sonic.net
Thu Jun 9 16:19:50 PDT 2011

Hi Lihong,

   The sym command in Chimera can also make copies of molecules and 
display them as surfaces.  I've attached an image where I made 5 copies 
of fibrinogen 1ei3 into a filament with the following commands:

     open 1ei3
     sym #0 group t,5,280 axis 1,0,.4 coord #0 surf true

The spacing of the copies is 280 Angstroms along direction 1,0,.4 and 
the copies are shown as surfaces.  This makes a model whose style can be 
changed with the multiscale dialog and I changed surface resolution to 3 
Angstroms and showed one copy as ribbon.  I tried 500 copies and Chimera 
had no trouble with it -- took a few seconds to create and then rotated 
at several frames per second.

   Here's an actin filament network that was made by putting REMARK 350 
BIOMT matrices in a PDB file of an actin monomer and also the ARP2/3 
junction complex.


The matrices were generated by a script to make a branching tree structure.



> Dear Lihong and others,
> The Multiscale Models tool in Chimera is meant for this purpose  --- it shows low-resolution surfaces, which are often preferred for large complexes.
> In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog.  This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains.  You can adjust the colors, surface resolution, etc. in the dialog.  Click the dialog's Help button to see its manual page.  There is also a copy here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
> I also tried it with 1m1j, which also worked fine on my computer.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 9, 2011, at 12:13 PM, Russell M. Taylor II 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://plato.cgl.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<protofibril.zip>_______________________________________________
>> Chimera-dev mailing list
>> Chimera-dev at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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