Hi XY, No -- if I understand correctly, the CDD has sequence alignments imported from outside sources (other databases) as well as human-curated alignments. I wasn't sure whether you meant sequence alignment or 3D structure alignment, but you can save the CDD sequence alignment as a file and then open it in Chimera. You could also open the structures and then tell Chimera to superimpose the structures using the CDD sequence alignment. For example, if I go to this page with a curated CDD sequence alignment: <http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=132758> … I can go down to the Sequence Alignment section, choose format mFasta, click Reformat, then copy and paste into a plain text file named (for example) cdd.fa, attached. I can see that there are some structure sequences in the alignment, including 2ax9, 1xj7, 1t73, ... In Chimera, I can open cdd.fa and PDBs 2zx9, 1xj7, 1t73. In the sequence window menu: Structure… Match will bring up a dialog for superimposing the structures using the sequence alignment. 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 May 10, 2014, at 4:56 AM, ce <allderann@gmail.com> wrote:

Hi, Does Chimera constain an algorithm that can generateconserved domain alignment in the exact way as Entrez CDD alignment works ? Yours sincerelly, XY