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.

Von: Joćo Rodrigues []
Gesendet: Freitag, 27. Januar 2012 09:56
Bis: James Starlight
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.

Joćo [...] Rodrigues

No dia 27 de Janeiro de 2012 09:50, James Starlight <> 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 ?


2012/1/27 Thomas Holder <>
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:

The atoms must both be within the same object.


Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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