On Jul 26, 2014, at 4:49 AM, Marek Basler marek.basler@gmail.com wrote:

Hi, I'd like to be able to change an association between a sequence in a multiple sequence alignment and an opened structure model by a chimera command. I have a model that is a multimer and I'd like to color code one of its subunits according to its sequence conservation ... but I need to reassign the automatic association that Chimera does after opening of a fasta file.

Strictly speaking, there is no command for this -- you have to use Python code to get exactly what you're asking for here. However, one thing you can do is to use the "split" command to split the chains of your model into separate models and then open your alignment file -- each chain that can associate with the alignment then will associate with the alignment.

Depending on what the rest of your script is doing, "split" may or may not prove to be a workable solution. If splitting the model is problematic for the rest of your script, let me know and I will send you a Python script to achieve the association you need. You'll be able to run the Python script just by using the "open" command in your regular script.

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu