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
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
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
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
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
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
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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