Controling the configuration of chiral atoms.
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.
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.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 www.click2drug.org On Thu, Apr 7, 2011 at 8:19 PM, Eric Pettersen <pett@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Eric Pettersen -
vincent zoete