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] 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

Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread Thomas Holder
Hi James, the modeling capabilities of PyMOL are rather limited, there are probably more powerful tools for such tasks. Without guaranty that the result will be reasonable, try this: # lock all but the STG tripeptide protect not pepseq STG # activate sculpting sculpt_activate all set

Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread Jed Goldstone
James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you

Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread James Starlight
Dear Thomas, Jed! Firstly, thanks for the advise in further days I'll try Modeller software! But also I've tried to use above advises in PyMol and in general I was satisfy with the results. I have just only several questions 1- What exactly is the Sculpping ? As I've understood its something