[Chimera-users] Reg: Hydrogen Bond Analysis

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 25 15:13:29 PDT 2013


Hi Nadir,

Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria  are things that can be measured or calculated by molecular graphics & analysis programs.  For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs.

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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote:

> Hi Elaine,
> 
> I addressed the question to CCP4BB but il did not seem to interest anyone.
> I state it again :
> 
> I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC.
> Ref:
> "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein,
> Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary,
> Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza,
> Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci,
> and David J. Nesbitt
> Pure Appl. Chem., Vol. 83, No. 8, pp. 1619–1636, 2011.
> doi:10.1351/PAC-REP-10-01-01
> © 2011 IUPAC, Publication date (Web): 8 July 2011
> Defining the hydrogen bond: An account (IUPAC Technical Report)*"
> 
> 
> Tough job, isn't ?
> 
> My guess is that Chimera should be involved.
> 
> Nadir Mrabet
> 
> 
> Dear Elaine,
>                 Many thanks for the suggestion and reply. I will do as said
> and will mail if any problem persists.
> 
> On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Dear Amit,
> > Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities.  Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
> >
> > There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
> >
> > You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above.
> > I hope this helps,
> > 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
> >
> >> Dear Chimera Users,
> >>                           I am new to chimera and I have some
> >> protein protein interaction results to be analysed. Most of
> >> the results are from HADDOCK server which gives a
> >> protein protein complex. So, is it possible to visualize
> >> the hydrogen bonds formed between the proteins using
> >> chimera? If yes, how? I am eagerly waiting for the answer.
> >>
> >
> 
> 
> 
> -- 
> 
> Yours Sincerely,
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~
> Amit Jaiswal,
> Department of Bioinformatics,
> School of Life Sciences,
> Pondicherry Central University,
> Kalapet, Pondicherry,
> Puducherry - 605 014.
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~
> 
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