Hi Stefano, If you really want to specify atoms by serial number, and do it many times, you could do that with a Chimera command script, e.g. color red @/serialNumber=4 or serialNumber=8 or serialNumber=10 color red @/serialNumber=20 label @/serialNumber=20 color goldenrod @/serialNumber<100 and serialNumber>20 color dodger blue @/serialNumber>100 These are the same commands that could be entered at the Command Line (show using Favorites... Command Line) -- you can test them there. Then just put all the commands you want into a text file, the Chimera command script. Just opening the script (named *.com or *.cmd) would execute the commands. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descrip...

However, there are many other ways to specify atoms besides serial number that might be easier: atom name, residue name and number, values of other attributes such as element or bfactor, etc. color red :25.a,43-57.a@ca (alpha-carbons of residues 25 and 43-57 in chain A) color red @/bfactor>50 (all atoms with B-factor >50) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html

Some other approaches that would give you more flexibility in coloring: - create your own aliases, for example alias clust1 :25.a,43-57.a alias clust2 :1-24.a,1-40.b color red clust1 color dodger blue clust2 - create your own new attribute, for example named "clusterNumber" and assign values 1,2, ... then just use commands like color red @/clusterNumber=1 More on how to create your own attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...

You can still use serial numbers when creating the aliases or defining a new attribute if that is the most convenient specifier. 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 Sep 21, 2009, at 7:02 AM, Stefano Meliga wrote:

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster.

I would like to plot the clusters in different colours.

I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n

Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano