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<mailto: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<mailto: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
:-)
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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