[Chimera-users] HBONDS comparing GROMACS and CHIMERA

[Eric Pettersen]

Hi Tasos,
	I would think that reading the paper the code is based on would be clearer than reading the code based on the paper, but I guess you can judge that for yourself.  The code is pure Python and is shipped with every distribution of Chimera.  It's in <your Chimera installation>/share/FindHBond/base.py.  On a Mac, add "/Contents/Resources" in front of "/share".

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On May 30, 2022, at 8:48 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> Forwarding to the list so that somebody who knows more about the code can answer...
> 
>> On May 30, 2022, at 1:23 AM, Sourpis, Anastasios <asourpis at uni-mainz.de> wrote:
>> 
>> Dear Elaine,
>> 
>> I would like to ask you if 
>> CHIMERA is openned source.
>> 
>> And if yes how can I have access to the Hbonds 
>> class/funtion to understand better how it works?
>> 
>> Kind regards,
>> Tasos
>> 
>>>> On May 25, 2022, at 11:32 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Dear Tasos Sourpis,
>>>> It is not surprising that different programs give (partially) different results, because each program uses somewhat different methods and/or parameters to identify H-bonds.  There is no universally accepted exact method.  However, my guess is that they would agree in the majority of cases.
>>>> 
>>>> The method used by Chimera is described in the help page:
>>>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
>>>> 
>>>> To summarize, there are several different distance and angle cutoffs depending on the atom types (element and hybridization state) of both the donor and acceptor.   The diagram of how the angle is defined would also depend on both of those types.
>>>> 
>>>> So probably what you are interested in are the exact diagrams for the different donor-acceptor pair types and the cutoff values for distances and angles.  These are in the figures and tables of the paper cited in the link above, namely
>>>> 
>>>> Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.
>>>> 
>>>> Then Chimera allows adding tolerance values to the cutoffs of distances and angles from the paper, because they were defined on very high-resolution crystal structures, but used on structures that may not be so precise.
>>>> 
>>>> I hope this helps,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.                       
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>> 
>>>>> On May 25, 2022, at 2:57 AM, Sourpis, Anastasios via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>>> 
>>>>> Dear All,
>>>>> 
>>>>> I would like to ask about the hydrogen bonds' built-in configuration
>>>>> of CHIMERA. 
>>>>> 
>>>>> Can I possibly have some insight into how it works?
>>>>> 
>>>>> Regarding the distance and angle constraints do you have any 
>>>>> graphical representation of the conditions.
>>>>> 
>>>>> I would like to attach a figure and ask if this is the correct
>>>>> applying configuration regarding the distance and the angle
>>>>> (hbonds_lst.pdf).
>>>>> 
>>>>> 
>>>>> Also, I would like to share with you the output 
>>>>> when I compare gmx hbond using GROMACS and 
>>>>> chimera.
>>>>> 
>>>>> ATTENTION: using gmx hbond I have the connected atoms 
>>>>> via hydrogen, but the two configurations are essentially 
>>>>> different (chimera_(molecules).tga and gromacs_atomonly.tga).
>>>>> 
>>>>> Thank you in advance.
>>>>> Kind regards,
>>>>> Tasos Sourpis
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users