Dear PyMol users!
I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?
James
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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,
Th
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
benz
Also I've tried to test set_dihedral command but failed
:)
E.g I want to change PHI value ( the angle beetween H-N and C-alpha-C-beta
in the residue)
I've type
set_dihedral resi 40 and name H, resi 40 and name N, resi 40 and name
CA, resi 40 and name CB, -30
and obtain error
Selection 1 does
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
1- What exactly is the Sculpping ? As I've understood its something like
real-time minimisation of the edited structure. Is what cases this might
be better than rigid rotation\edition of the selected bonds/ angles by
mouse-mode editing ? :)
It's a geometry optimizer. It has bond/angle/torsion/vd
I have a weird problem: we have a cluster of Linux computers (managed
by Sun Grid Engine) running at least three different distributions of
Fedora. I compiled PyMOL on the head node (Fedora 8) and I want to
invoke it on the command line to generate images as part of some other
computations. I'm u
