I don't want to hijack the thread but I was curious if you can point to few pymol features for generating and rotating molecules and how they would play with other tools. For example, if I just go download pdb files or take output from DFT, it may be easier to do analysis with certain alignments. Similarly, I want to generate hypothetical molecules for various tests and wanted some easy way to do that. There are many graph, shape, or geometry tools available in various fields, maps, CAD etc and apparently they are tools for drawing or editing molecules. However, I was just looking for something that works from command line and is reasonably easy to integrate with other things.
Apparently pymol is all based on python and presumably features, like the plugins you pointed me to earlier, are easy to mix and match with other tools but not sure offhand how to approach this. Right now, I'm making my own c++ tool using Tcl front end so that I can eventually use all the math libraries like lapack and boost as I want to do larger molecules( and use these for various types of "alignments" that could generate large matricies ). Should I use python or just use something that pymol already has? The immediate need is just to generate xyz files that look like short polyenes and be able to perturb them using a script. So for this I end up with Tcl input that looks like a list of atom and direction commands but there is probably some way to do this much with existing tools. Thanks. ---------------------------------------- > From: jason.vertr...@schrodinger.com > Date: Tue, 11 Dec 2012 07:38:32 -0600 > To: jonat...@strubi.ox.ac.uk > CC: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Help with alignments > > Hi Jon, > > align prot1 and chain A, prot2 and chain X > > 'super' and 'cealign' should work similarly. > > Cheers, > > -- Jason > > On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes > <jonat...@strubi.ox.ac.uk> wrote: > > > > I am wanting to align proteins based on superposition of > > particular chains. Is it possible to do the superposition based > > on the chains, but to move, in this case the entire complex ??? > > > > Thanks > > Jon > > > > Sent from my iPad > > > > ------------------------------------------------------------------------------ > > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > > Remotely access PCs and mobile devices and provide instant support > > Improve your efficiency, and focus on delivering more value-add services > > Discover what IT Professionals Know. Rescue delivers > > http://p.sf.net/sfu/logmein_12329d2d > > _______________________________________________ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
