August 2004 - Chimera-users - RBVI Mailing Lists

ribbons of nucleic acids
by Ann Mullin 01 Sep '04

01 Sep '04

Hello, I am wondering how to adjust the ribbons of nucleic acids so that they follow the path of the phosphates or the sugars, anything but the averaged path they have now. I want to show the backbone as a ribbon with bases projecting out, but now some bases float about the backbone. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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Chimera and building molecules
by Elaine Meng 31 Aug '04

31 Aug '04

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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. meng(a)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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building molecules
by Ben Schuler 31 Aug '04

31 Aug '04

Dear Chimera developers, It seems to me that the manual formation of bonds and building of any type of molecules (not only proteins and nucleic acids), which was a strength of MIDAS, is not supported by Chimera. I would very much welcome an implementation of these features to make Chimera a real replacement for MIDAS. Ben __________________________________________________ Prof. Ben Schuler, PhD Biochemisches Institut, Universität Zürich Winterthurerstr. 190, CH-8057 Zürich Tel: +41 44 635 5535, Fax: +41 44 635 5907 Web: www.biochem.unizh.ch/schuler Email: schuler(a)bioc.unizh.ch

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Chimera-users August 2004