[Chimera-users] Drawing a set of spheres describing a pocket in a protein

[Tom Goddard]

If Elaine did not give you enough options, here is one more.  You can write an XML Chimera marker file (suffix .cmm) that specifies sphere positions, radii and colors as described in the Chimera documentation that can be read in directly.

	https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles>

  Tom

<marker_set name="my spheres">
<marker id="1" x="-6.1267" y="17.44" z="-3.1338"  radius="0.35217" r="0" g="1" b="1"/>
...
</marker_set>




> On May 26, 2022, at 2:16 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 
>> On May 26, 2022, at 12:48 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> [...] make a PDB file where the spheres are fake atoms [...]
>> 
>> However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": 
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> 
> Correction: a better/easier way than "setattr" to change atomic VDW radii in Chimera is with the "vdwdefine" command:
> 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>
> 
> Best,
> Elaine
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