On Mar 30, 2010, at 9:04 PM, Elaine Meng wrote:
However, there are some issues that may affect whether you decide to use Chimera to calculate these values for your structures:
(1) You would need to run Match->Align for each pair. There is no option to do all pairwise comparisons on multiple structures. You would need to script looping through all pairs (with python or shell scripting).
(2) There is no Chimera command for Match->Align. Thus Match->Align would also need to be run via python. I don't have scripting expertise, so someone else would have to provide more details if you decide to try this.
Given that you said you wanted a complete pairwise matrix of ~50 structures, that would be ~1200 unique pairs, which is obviously way too many to do by hand. Currently Match->Align is awkward to script, even in Python, since all the important code is internal to the Match->Align dialog and basically impossible to call externally. If you are sure that you would like to use Chimera for this computation I can reorganize the Match->Align code so that it could be called externally. I don't think the reorganization will be difficult. You would still need to resort to a Python script to make the Match->Align calls and loop through your models, so you would need some rudimentary familiarity with Python. Let me know.
--Eric