Hi Shafrir, (1) The write command that you gave should have worked to write the file without bringing up a save dialog. I just tried this in version 1.2199 on the mac and it worked correctly. You could send more information on this problem (version used, platform, any error messages) to chimera-bugs@cgl.ucsf.edu Although there is no command to split a model in the released Chimera, you can download an "experimental feature" to do it. Instead of putting a *selected* chain into a different model, however, it puts each chain in the original file into a separate model. The split command is about the fourth thing on the experimental features page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Actually, I'm not sure what your script is doing, so another possible approach would be to delete the rest of the chains, resulting in a model with only your chain of interest. For example: command> sel :.a command> sel invert sel command> delete sel (2) To assign secondary structure arbitrarily (without using the ksdssp program), select the residues of interest, and click the button on the lower right corner of Chimera to open the Selection Inspector. In the Selection Inspector, change to Inspect Residue, then set "in helix" to false and "in strand" to true. If you wanted to save (write) the file for later, the changed assignments will be reflected in the HELIX and SHEET records. I hope this helps, Elaine p.s. no need to send the mail twice (delay is only because our moderator has to approve the message sometimes) On Apr 7, 2006, at 1:17 PM, Shafrir, Yinon ((NIH/NCI)) [F] wrote:

Hi there!

I have two questions regarding using Chimera.

How do you break a molecule to different models using the command line?

I have a protein composed of 4 chains. It loads as one piece and designated model 0

I then select a single chain and I want to designate it as a new model. How do I do that using the command line (so I can write a script)?

Also, when I select the chain and use the write command in this manner “write selected su1.pdb” the save dialog box pops up (even though I designated a filename)

When I try “write selected 0 su1.pdb” nothing happens.

My other question is:

How can you force chimera to assign secondary type display to residues without editing the PDB file first?

Say I want to show 30 residues that are not detected by ksdssp as beta sheets. Still, I want to represent them as beta sheets. Do I need to edit the pdb file?

Best regards

Yinon Shafrir

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

----- 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 Apr 7, 2006, at 1:17 PM, Shafrir, Yinon ((NIH/NCI)) [F] wrote:

Also, when I select the chain and use the write command in this manner “write selected su1.pdb” the save dialog box pops up (even though I designated a filename)

When I try “write selected 0 su1.pdb” nothing happens.

Elaine covered most of the answer here. Just a couple of things... The first write command you mention is missing the model number. So Chimera interprets "su1.pdb" as the model number (which is obviously kind of stupid) and the file name as missing, so it brings up a browser. I'll fix things so that it does some sanity checking on the "model number" and issues a syntax error in this case. The second write command probably did work but silently. I'll add a status message when the write command succeeds so that it doesn't seem like nothing happened. Also, the file gets written into the "current working directory", which may not be anyplace useful on Windows or the Mac, so on those platforms you may want to specify a complete path name for the file (or use the browser version of the command). --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu