Hi Peter, No problem - the features are documented, but there is no tutorial that includes adding a sequence. I tested the following with the most recent snapshot (1.2352, March 2007). (1) Open your sequence alignment in Chimera. I just found the following problem when testing the procedure: *if you created the sequence alignment with Match->Align, it is necessary to save it to a file (File... Save As from the Multalign Viewer menu, pick any format), quit from the alignment, and reopen it in Chimera (File... Open in the main menu) before you can add a sequence to it* ...this will be fixed in the next release, however. If the sequence alignment was already read from a file, no extra step is needed. (2) Choose "Edit... Add Sequence" from the Multalign Viewer menu and paste the new sequence in the dialog. Enter a name for the sequence, adjust the alignment parameters as desired, and click OK. Look at the alignment and decide whether it seems reasonable. If not, you can use "Edit... Delete Sequences/Gaps" to remove the sequence and try realigning it with "Edit... Add Sequence" and different alignment parameters. For example, if the sequence is fairly distantly related to the others, you may have better luck with blosum-30 than blosum-62. Editing is described here http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#editing (3) If they are not already open, open one or more structures that associate with the sequence alignment. (4) Once your new sequence is aligned with the others to your satisfaction, you can draw out boxes on the alignment using the mouse. If the boxes enclose parts of the sequence(s) that are associated with the structure(s), the corresponding parts of the structures will be highlighted (selected). Or, you can go the other direction by selecting parts of the structures and seeing where they are in the alignment. These forms of crosstalk are described here http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#crosstalk and in the "Sequences and Structures" tutorial. You can also show the secondary structure assignments on the alignment with "Structure... Secondary Structure... show actual" (for those sequences associated with structures) or "show predicted" (for sequences without structures) Alternatively, if you already have a sequence alignment that includes your sequence of interest plus others that will associate with structures, you can just open them all in Chimera and skip straight to #4. Sometimes I get alignments from databases such as Pfam. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 13, 2007, at 2:27 PM, Peter Murphy wrote:
Thanks for the quick response Dr. Meng,
Thanks to your helpful tutorial, I now know how to align two structures and get an alignment. But I am interested in the ability to add a sequence (that doesn't have a structure) to the alignment and see if/where parts of it map onto the structures. Is there such a tutorial on your website, or might you be able to give me a quick rundown :P
Thanks again
-- Peter Murphy, B.Sc., M.Sc Candidate Atlantic Research Center Dalhousie University Halifax, Nova Scotia, Canada