[chimera-dev] congratulations to the new beta release

[C. Klein]

Hi Eric, 

hmm, Midas.... I have used this "command language" and also the "atom
specifiers" once in a while, but not too often. In general, I find it
useful to have such a thing (because it allows you to
simplify/automatize certain tasks). The problem is, as always, that I am
reluctant to learn yet another "language". 

Concerning the specific problem of numbers and atom specifiers: it would
certainly be sufficient for my purposes to access this function via the
menu. I think that most other modeling programs have this display
option, thus I am probably not the only person that needs it. 

If you were to ask me about general future wishes, then a "build
molecule" and "write file" functionality would be on top of the
wishlist. I know that this would be a major project. You would first
have to decide on the file format: pdb is probably the most generic one.
The swisspdb-viewer team decided on an extension to the pdb format
(SPDPV lines added to the bottom of a regular pdb file) which contains
spdbv-specific information on display and selection status. That is a
good idea, because it allows you to read that particular file with
practically all other modeling programs. 

The mol2 format is probably much more difficult to implement, but would
be the second most important on my list, because it has become sort of a
"lingua franca" for small molecules, and because it contains so many
useful possibilities to store information. It is also the preferred (or
the only possible!) input for all the "independent" docking programs
(dock, autodock, gold ....). I am just having a major problem to connect
accelrys software and these docking programs because accelrys "ignores"
the mol2 format, that is giving me a big headache....

Best wishes, 

Chris