[Chimera-users] Reg: Hydrogen Bond Analysis

Francois Berenger berenger at riken.jp
Sun Mar 24 18:31:45 PDT 2013


In case you don't get enough from Chimera, I think pisa from CCP4mg is 
specialized in analyzing protein interfaces.

http://www.ccp4.ac.uk/MG/ccp4mg_help/pisa.html

On 03/24/2013 03:32 AM, Amit Jaiswal wrote:
> 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.
>>>
>>
>
>
>



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