Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir