Is it a small organic molecule or a modified amino acid within the context
of a protein?
2012/1/29 Tim Schulte <tim.schu...@ki.se>
> Dear James,
> I agree with Joao, for fast and dirty minimisation you might try the
> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
> molecule the Prodrg server is the way to go.
> Cheers,
> Tim
> ------------------------------
> *Von:* João Rodrigues [anar...@gmail.com]
> *Gesendet:* Freitag, 27. Januar 2012 09:56
> *Bis:* James Starlight
> *Cc:* pymol-users@lists.sourceforge.net
> *Betreff:* Re: [PyMOL] Editing of the pdb structure
>
> 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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>
>
>
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--
======================================================================
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tev...@bioacademy.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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