[chimera-dev] AddH etc.

[Elaine Meng]

Hi Timm,
Thanks for the compliments!  Chimera is under active development, and
some of your suggestions are already on the "to do" list.

(1) The best news first:  atom deletion has already been incorporated and
is now available in the snapshot version created earlier this month
(can be downloaded by following links from the Chimera home page).
You may wish to wait for the full production release, however, since we
plan to make one next week.

How to delete atoms: either use the menu item
    Actions... Atoms/Bonds... delete
to delete the currently selected atoms (careful!)
or the command
    delete [atom-spec]
for example, 
    delete element.H
(delete all hydrogens)

This example also shows that atom specifications have been made more powerful.
In the newer (October 2003) versions, you can use several menu items under
Select (such as "element.H", the entry H under Select... Chemistry... element,
or even just "H") as atom specifications.

Atom deletion is also really useful when you want to get rid of solvent
or extra chains that you are not going to look at.

(2) Coming soon: consideration of metal coordination and H-bonding networks
when hydrogens are added (AddH).  We will note your e-mail address (Timm)
and let you know when this is available in a snapshot version of Chimera.

(3) On the "to do" list, but long-term: simple molecule editing (building) and
minimization capabilities.  I know I'd like to do these things, but adding
them is nontrivial.
Thanks for your comments,
Elaine
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Elaine C. Meng, Ph.D.
Computer Graphics Lab and Babbitt Lab
meng at cgl.ucsf.edu
http://www.cgl.ucsf.edu/home/meng/index.html
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