Hi Hong, 1. Yes, you can definitely get rid of the parts you are not interested in. (A) Your example is an NMR structure, where the PDB file has multiple models. If you open the Model Panel (under Favorites) you can see the numbering of those models: for 1x95, there are models #0.1-0.15. In the Model Panel, click the line on the left for the structure you want to keep and then click "show only" on the right; this hides all the others. Or, if you really want to delete the others instead of just hiding them, choose their lines (using clicking, dragging, and/ or Ctrl-click to add/subtract) and then click "close" on the right side of the Model Panel (NOT the Close button at the bottom of that panel!). Or, you can do it in one step with a simple command; the following example keeps #0.1 and deletes the others: delete #0.2-end (B) Sometimes there are more chains than you want even in a single model. In that case, you can select the parts you want to delete and then use "Actions... Atoms/Bonds... delete", or select what you want to keep and then invert the selections with "Select... Invert (all models)" before deleting. Similar to the example above, you can also use the "delete" command. 2. Chimera does not build DNA/RNA, although we would like to add that in the future. The following web server will build nucleic acid helices (I haven't tried it yet): http://structure.usc.edu/make-na/ It probably would just build the whole thing rather than adding to an existing structure, however. 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 May 8, 2007, at 10:01 PM, Hong Liang wrote:
1. If a pdb file contains more then one struture, how can I select and keep just one and get rid of the rest. Such as 1X95. It is a big mess after Chimera load the the DNA pdb structure. How can I leave just one double helix? 2. Can Chimera do the extension of DNA. Such as 1X95 has the hexamer with the sequence of ATGCAT, can Chimera double it to a dodecamer with a sequence ATGCATATGCAT? It Chimera can not do that, do you know which software has such a function. I tried PyMol but did not get what I wanted.