Re: [PyMOL] Editing of the pdb structure

2012-01-27 Thread James Starlight
Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? James -- Try before you buy = See our experts in action! The most comprehensive online learning library

Re: [PyMOL] Editing of the pdb structure

2012-01-27 Thread 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: http://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers,

Re: [PyMOL] Editing of the pdb structure

2012-01-27 Thread James Starlight
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

Re: [PyMOL] Set values for dihedral angles

2012-01-27 Thread James Starlight
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

Re: [PyMOL] Editing of the pdb structure

2012-01-27 Thread João Rodrigues
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

Re: [PyMOL] Set values for dihedral angles

2012-01-27 Thread Thomas Holder
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

[PyMOL] single pymol installation, multiple OSes

2012-01-27 Thread Nat Echols
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