I recall a command-line tool from my student days ('88-'92) that I used for molecular construction and editing. I wish I could remember the name of it as I'd love to track down the code for this. It was available on VMS before BIOSYM started up. I believe BIOSYM included it in their package, but this component was actually free. (I could be wrong as this is a long, fuzzy memory!) I recall the command line interface as being simple and very easy to use. I vaguely recall you could just type in an amino acid sequence, assign secondary structure and you were done. Side chains could be "mutated". DNA could be built also. I doubt this program could handle anything other than "standard" amino acids and bases, but if I had the code I could try fiddling (for my own use at any rate). If anyone is able to name the program, I'd be interested in tracking it down. Part of the reason I mention this here is that this is another way forward - find an external program start from there. Grant

Dear Ben, We definitely agree that molecule-building would be a very useful addition to Chimera. Toward this functionality, Chimera includes hydrogen addition; also, the "bond" command has been implemented (and will be available in the next release). Chimera also includes the "swapaa" and "swapna" commands which "mutate" one sidechain or base to another, although they are not very sophisticated.

I am not certain what you are referring to in MIDAS, which only had very rudimentary building capabilities and no ability to add hydrogens. The "addgrp" command did allow definition of new amino acid sidechains, but was quite unwieldy and not usable for building in general. Similarly, "addaa" could append one of the standard amino acids to the end of a peptide but was not generalizable to other types of molecules.

If you could clarify how you were applying these tools, we might be able to prioritize developments accordingly. Thank you, Elaine

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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

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