Dear Liuqing Chen, We don’t have secondary structure symbols, but there are other symbols as shown in the figure in this section of the manual page: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers

The definition file format is fully described here, and it is a simple text file that you can easily make by typing into your favorite text-editing program. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat

As it says, the shapes are circle, square, diamond and star. The only tricky thing is that the data lines have tabs in them, which is why I don’t just show a 3-line example file right in this e-mail. I attached one (simple.hdr) so you can see how simple it is. but you have to first open some sequence or alignment and then open this definition file ( sequence window menu: Headers… Load). It will show a blue star at the 3rd position of the sequence or alignment, as in the attached image. 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 Mar 30, 2017, at 7:51 PM, 陈柳青 519198561@163.com wrote:

Dear all ! Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? thanks! Liuqing Chen