Dear James,
As someone has told you already, Pymol is a visualization tool, not a
modelling suite. I guess you would be better off using something like
AMBERTOOLS or MODELLER, depending on what you want to model, or any other
"real" simulation/modelling package otherwise your results are very weak...
My opinion only.
João [...] Rodrigues
http://nmr.chem.uu.nl/~joao
No dia 27 de Janeiro de 2012 09:50, James Starlight
<jmsstarli...@gmail.com>escreveu:
> Arne, Thomas
>
> Thanks alot. Bond works finw
>
>
> I'd like just to ask what about geometry optimisation of the new structure
>
> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
> from 1.5 A from each other.
>
> When I've create new bond by bond command new ring look like 6memb ( like
> benzol) because of long distance between adj atoms.
>
> How I could optimise geometry of the new mollecule? Have pymol some
> built-in functions like conformational search be means of monte carlo or
> energy minimisation ?
>
>
> James
>
>
> 2012/1/27 Thomas Holder <spel...@users.sourceforge.net>
>
>> On 01/27/2012 09:11 AM, James Starlight wrote:
>>
>>> Dear PyMol users!
>>>
>>> I need to create NEW covalent bond between two adjacent atoms. How this
>>> could be done in PyMOl?
>>>
>>
>> you could have guessed it:
>> http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
>> :-)
>>
>> The atoms must both be within the same object.
>>
>>
>> Cheers,
>> Thomas
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
>
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