[Chimera-users] saving spheres

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 4 09:26:21 PDT 2012

Hi Mary,
In Chimera each cluster is a different model (something like model numbers #0.1, #0.2, #0.3, ...), so if you wanted to write two clusters as a single cluster, you would first need to combine them into a single model (for example, #0.1 and #0.2 could be combined into a new model #1).

You can see what models are present by looking in the Model Panel (in menu under Tools.. Favorites), and you can combine models by using the Model Panel function "copy/combine".

For details, see "Editing Sphere Clusters":

Alternatively, instead of using Chimera, you could just text-edit the sphere file to put all the spheres in a single cluster.  The sphere file has lines like:

cluster     3   number of spheres in cluster    50

...and you could just remove the second such line and update the sphere count in the first such line to include all the spheres in the file.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 3, 2012, at 11:18 PM, MARY VARUGHESE wrote:

> Hi,
> I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion.
> Thanking You.

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