[chimera-dev] congratulations to the new beta release

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 22 11:20:23 PDT 2002

Hi Chris,

Just a couple of further thoughts.  As Elaine pointed out, the next release 
of Chimera (late October) will have saving-to-PDB available via the midas 
"write" command.  Depending on other priorities, I may have to time to 
implement it also as a button in the model panel in time for the release, 
otherwise that will be in the following release.  Saving sessions is now 
available in the "File" menu, though structure modifications (e.g. bond 
rotations) aren't saved in sessions yet.

Saving to mol2 will also get done in the not-too-distant future, but mostly 
likely not by the next release.  Maybe 50/50 for the following release.

We have no plans to implement real structure building.  We do allow 
swapping of amino acid / nucleic acid side chains via the midas 
"swapaa/swapna" commands, which still need some improvement though.  Good 
structure building is a lot of work and other packages (e.g. Spartan, 
ChemDraw) do it so well that we'd prefer to work on things other packages 
don't have rather than re-invent a very round wheel.  I guess this is kind 
of similar to the Delphi thing where we felt that it was better to 
integrate to an excellent external implementation rather than expend the 
many man-months necessary to make an implementation of similar quality in 
Chimera.  In this case we wouldn't integrate per se but instead just 
suggest getting some package that does structure building and read the 
structure into Chimera normally.

Whenever any other suggestions occur to you, make sure to drop us a line!


On Thursday, August 15, 2002, at 12:12 AM, C. Klein wrote:

> 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
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