[Chimera-users] Controling the configuration of chiral atoms.

vincent zoete vincent.zoete at gmail.com
Thu Apr 7 23:17:40 PDT 2011

Hi Eric,

Thank you very much for considering this addition!
I am looking forward to use it :)

Have a nice day,

Vincent Zoete,
Molecular Modeling group - SIB

On Thu, Apr 7, 2011 at 8:19 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Vincent,
> I'm glad you're happy with Chimera (mostly ;-) ).  Sure we would consider
> it.  The Build Structure tool is one of those "second line" features that I
> work on improving as time permits.  I will open a feature-request ticket in
> our database with you and Dr. Maroun on it so that you both will be notified
> when it gets implemented.  It will probably happen in the same 1.6-1.7 time
> frame that I mentioned in the mail to Lucio yesterday, though it happens
> that upon reflection his feature was easy enough to implement that I just
> went ahead and did it today.  I'm thinking that chirality inversion will be
> a tad more difficult, so my time estimate may be more realistic this time
> unfortunately!
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Apr 6, 2011, at 11:49 PM, vincent zoete wrote:
> Dear Chimera team,
> We are very satisfied daily users of Chimera for drug design and
> protein engineering applications in our lab. Congratulations for your
> great work!
> I would like to come back on the point raised by Dr. Charbel MAROUN
> recently. Having the possibility to change the configuration of
> whatever chiral atom would be very useful for drug design
> applications. It's true that we can do it using other software like
> Pymol or HyperChem, to cite just two of them arbitrarily. But it would
> be much more convenient to rapidly and graphically do it in Chimera,
> without the need to switch to another program for that particular and
> single action.
> We are often working with D-amino acids and chiral small molecules. We
> apreciate a lot the "Build Structure" module to construct or modifiy
> such compounds, and allowing more control on the chiral center
> configuration would be very useful.
> Do you think you could consider adding such chirality inversion
> command in the future?
> Sincerely,
> Vincent Zoete,
> Molecular Modeling group - SIB
> www.click2drug.org
> ===========================================================
> Hello,
> Sorry, Chimera does not do that.  I am pretty sure that SYBYL and
> probably some other programs will do it, but you may want to ask on a
> more general list such as CCL.net for a more certain and detailed
> answer about other programs.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jan 28, 2011, at 6:15 AM, R. Charbel Maroun wrote:
> Hi everybody,
> Is there an easy and quick way to invert the chirality of an atom, say a Ca
> ?
> Greetings,
> -----------------------------------------
> R. Charbel MAROUN, Ph.D., H.D.R.
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