From: Thomas E. <te...@gm...> - 2012-01-30 09:53:26
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Is it a small organic molecule or a modified amino acid within the context of a protein? 2012/1/29 Tim Schulte <tim...@ki...> > Dear James, > I agree with Joao, for fast and dirty minimisation you might try the > program Chimera or VegaZZ. If you just wanna have an energy-minimized small > molecule the Prodrg server is the way to go. > Cheers, > Tim > ------------------------------ > *Von:* João Rodrigues [an...@gm...] > *Gesendet:* Freitag, 27. Januar 2012 09:56 > *Bis:* James Starlight > *Cc:* pym...@li... > *Betreff:* Re: [PyMOL] Editing of the pdb structure > > 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... > > My opinion only. > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao > > > > No dia 27 de Janeiro de 2012 09:50, James Starlight < > jms...@gm...> escreveu: > >> 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 >> benzol) because of long distance between adj atoms. >> >> How I could optimise geometry of the new mollecule? Have pymol some >> built-in functions like conformational search be means of monte carlo or >> energy minimisation ? >> >> >> James >> >> >> 2012/1/27 Thomas Holder <sp...@us...> >> >>> 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<http://pymolwiki.org/index.php/Bond> >>> :-) >>> >>> The atoms must both be within the same object. >>> >>> >>> Cheers, >>> Thomas >>> >>> -- >>> Thomas Holder >>> MPI for Developmental Biology >>> Spemannstr. 35 >>> D-72076 Tübingen >>> >> >> >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: te...@bi... te...@gm... website: https://sites.google.com/site/thomasevangelidishomepage/ |