Hi Shuanghong, Question (1), surface problem: I don't think the problem where nothing happens when you type the command "surface" has been reported. Sometimes there is a delay while the surface is being calculated, but it shouldn't be terribly long. Problems have been reported in some cases, but they generally cause some sort of error message. To register a problem more formally, you could send mail to chimera-bugs@cgl.ucsf.edu and be sure to include what version of Chimera and what kind of computer you are using, and what structure(s) cause the problem. Question (2), writing out part of a PDB file: If you are on a **non-Windows** system, you can use the command "pdbrun" to save just the atoms that are displayed. You could display only the atoms you want by first selecting what you want to measure the distance to. Then, use Select...Zone... to select all the atoms in the region you want to write out. Then the command "show sel" will undisplay the rest of the stuff. (Or, instead of selecting you could do it all in one command, for example show :212.a za<4.5 for all atoms within 4.5 A of any atom in residue 212 of chain A. Specifying zones in the command line is described in the manual page on atom specification, which is listed in the Basic Functions index.) Next, use pdbrun (see man page using the command "help pdbrun"), for example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on **Windows** the only way I can think of is to actually delete the atoms/bonds you don't want to write out ("delete" command or Actions... Atoms/Bonds... delete). For example, when only what you want to write out is displayed, delete @/!display actually deletes the other stuff. Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng@cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=