Hello, Eric already mentioned the most important point: that this is only the format used within the Custom Residue Label dialog (opened with Actions... Label... residue... custom in the Chimera menu). The string starting with "wt" mentioned in your mail is just an example from the man page. If you didn't want "wt" in your label, of course, it shouldn't appear in that string. The Custom Residue Label dialog doesn't actually require anyone to type in those slightly ugly strings by hand, however. If you really wanted the label to be SER200 for example, you would just select that serine residue, open the dialog from the menu, and then click the buttons name number (in that order) and then Apply. Hope this clarifies - Elaine --- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu 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 Dec 1, 2004, at 7:43 AM, Stephen P. Molnar, Ph.D. wrote:

I have to admit to being completly flumoxed [sic] by this one!

How do I label an individual residue: According to help the format is:

wt %(1-letter code)s%(number)s

Now I have an enzyme, 1QTI.pdb in which I wish to label the SER200 label. I have tried every combination of the example on the help page that I can think of without success.

What is the exact format for creating that label?

Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hello Dr. Molnar, There are a multitude of different ways to make selections. Here is the general "selection" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html In brief, if you knew where it was on the screen, you could pick it with the mouse (Ctrl-click). If you only know the number you could select it in the command line: select :200 (if no chain ID), or select :200.a (if the residue is in chain A) (you have to give the chain ID if there is one, since there could be another residue 200 in some other chain). Yet another way is to use the sequence panel. (first open the Model Panel from the Favorites menu, and then in the Model Panel choose the model of interest on the left and click the "sequence..." button on the right). sequence panel man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html In the sequence panel: when you mouse over the sequence, the actual numbers in the structure are reported. You can just highlight (in the sequence panel) the residue you want; the default behavior is to select that residue in the structure. Hope this helps, Elaine On Dec 1, 2004, at 12:14 PM, Stephen P. Molnar, Ph.D. wrote:

Thanks, both you and Elaine, for your reply

First of all, I had made the Action selections you outlined below.

Now, I hate to be so dense (although, after a lifetime of practice at it, I think that I'm rather good at being dense), but how do I select the particular residue that I want to label in 1qti so that I can cut and paste the information. The reason that I want to label it in the first place is so that I can identify the residue in the graphics window. Certainly Select/Residue/Name lets me pick all of the serine residues in the protein, but I only want one of them labeled.

I hope that I haven't made my question even more murky than it origionally was.

Eagerly awaiting your further explanation.

Thanks in advance.

-- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry