Re: [PyMOL] morphing

2012-01-26 Thread Thomas Holder
Hi Hasan, if your structures are identical in sequence (same number of atoms), the direct way for morphing would be to load them into the same object in two states and then call rigimol.morph, like this: from epymol import rigimol cmd.extend('morph', rigimol.morph) load conf1.pdb, inobj, 1

[PyMOL] Set values for dihedral angles

2012-01-26 Thread James Starlight
Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by

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

[PyMOL] Access to pymolwiki

2012-01-26 Thread Troels Emtekær Linnet
I am not able to reach the site? Is it down? Troels Emtekær Linnet -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual

Re: [PyMOL] Access to pymolwiki

2012-01-26 Thread Jason Vertrees
Hi Troels, I can get to it. Still having problems? Cheers, -- Jason 2012/1/26 Troels Emtekær Linnet tlin...@gmail.com: I am not able to reach the site? Is it down? Troels Emtekær Linnet -- Keep Your Developer

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

Re: [PyMOL] Access to pymolwiki

2012-01-26 Thread Troels Emtekær Linnet
No. :-) Works as a charm now. It was a temporary thing for 10 minutes. Maybe my internet solution from the uni was a little strange. /T 2012/1/27 Jason Vertrees jason.vertr...@schrodinger.com Hi Troels, I can get to it. Still having problems? Cheers, -- Jason 2012/1/26 Troels