[Chimera-users] Capping a clipped sphere representation

[Michelle E. McCully]

The "conic" command was exactly what I was looking for!  I ended up using
the command:
conic -s -f ps -o test.ps

Thanks so much for your help, Elaine and Eric!
Michelle



On Sun, Jun 26, 2011 at 5:56 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Michelle,
>        If you're willing to use an image that is just atom spheres, i.e. no
> surfaces, volumes, BILD objects, etc. then you can use the "conic" command:
>
> http://www.cgl.ucsf.edu/**chimera/current/docs/**
> UsersGuide/midas/conic.html<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/conic.html>
>
> It will produce an image like the one I've attached.
>
> --Eric
>
>        Eric Pettersen
>        UCSF Computer Graphics Lab
>
>
>
>
>
> On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote:
>
>  Hi Michelle,
>> Sorry, Chimera doesn't have capping of atomic representations or ribbons.
>> However, you can achieve something similar to the "sliced spheres" by:
>>
>> (a) showing a molecular surface
>> (b) clipping and capping that surface (capping occurs by default)
>> (c) coloring the molecular surface to match the atoms (this occurs by
>> default)
>> (d) the nonobvious step: coloring the cap to match the atoms too, using
>> Color Zone
>>
>> See the picture here to get some idea if this will meet your needs:
>> <http://www.cgl.ucsf.edu/**chimera/docs/UsersGuide/**
>> tutorials/bfactor.html<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
>> >
>>
>> It sounds like you figured out (a)-(c).  Then open Color Zone (under
>> Tools... Volume Data), select the protein atoms (for example, command "sel
>> protein"), click "Color" on the Color Zone tool to color the MSMS surface
>> (which includes the cap).  Radius values >2.5 should all be fine, the
>> closest atom is used.
>>
>> However, at this point the coloring may look jagged. You could use a finer
>> triangulation of both the molecular surface and the surface cap to make the
>> former smoother, and get rid of jagged coloring edges in both.
>>
>> There are several ways of increasing the vertex density of a molecular
>> surface, but the easiest to describe in email is this command:
>> setattr s density 5
>> ... where the default density is 2.  You could try different numbers,
>> being aware that finer triangulations (higher density values) use more
>> memory and may make rotating the structure slower.
>>
>> To get a finer triangulation of the cap, start Surface Capping, for
>> example by clicking the "Surface capping..." button in the side view, and
>> increase the "Mesh subdivision factor," say to 3.
>>
>> Several of these steps are also covered in the "B-factor coloring" image
>> tutorial.
>> <http://www.cgl.ucsf.edu/**chimera/docs/UsersGuide/**
>> tutorials/bfactor.html<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
>> >
>>
>> 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 24, 2011, at 4:12 PM, Michelle E. McCully wrote:
>>
>>  Hi,
>>> I would like to create an image of a protein shown in van der Waals
>>> spheres with a clipped surface.  I'd like each individual sphere/atom to be
>>> capped and colored the same color as the atom.  Is this possible?
>>>
>>> I can show the protein in spheres and clip it using the side view dialog,
>>> but the clipped spheres show up as shells instead of solid balls.  I also
>>> have found directions for capping and coloring surfaces, but I don't see a
>>> way to make the clipped surface colored by atom.  It seems that building my
>>> protein out of sphere shapes and clipping that would give me the desired
>>> effect, but I was hoping there was something easier and built-in that I'm
>>> missing.
>>>
>>> Thanks for your help,
>>> Michelle
>>>
>>
>>
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>>
>
>
>
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