Anatoliy, I haven't yet tried a vector field. Can you share the raw data file?
Cheers, -- Jason On Wed, Apr 18, 2012 at 10:33 AM, Anatoliy Volkov <anatoliy.vol...@mtsu.edu> wrote: > Dear Jason, > > Thank you very much for your prompt reply. > > My program can already write out CCP4 maps > but only for scalar properties. That is, > for each (x,y,z) point there is single value (magnitude) > of some property. > > However, for a vector property, I have three > components for each point (x,y,z). > For example, for gradient (grad) of electron density (rho), > at each point (x,y,z), I have grad(rho)_x, grad(rho)_y, grad(rho)_z, > i.e. components of vector along x-, y-, and z-direction. > > I am not sure how to specify vector data in CCP4 header > http://www.ccp4.ac.uk/html/maplib.html > > In Amira, I can use AmiraMesh format to specify vector data. > For example, > > # AmiraMesh ASCII 1.0 > > define Lattice 51 51 51 > > Parameters { > BoundingBox -2.000000 2.000000 -2.000000 2.000000 > -1.883428 2.116572, > CoordType "uniform" > } > > Lattice { float[3] Data } = @1 > > @1 > 0.0000012264 0.0000007483 0.0000008691 > 0.0000017187 0.0000010925 0.0000012687 > 0.0000023678 0.0000015706 0.0000018239 > 0.0000032062 0.0000022235 0.0000025820 > 0.0000042665 0.0000030998 0.0000035996 > 0.0000055783 0.0000042559 0.0000049419 > ..... > > where each line contains x-, y-, and z-components of a vector > at each (xyz) point. > > Can I use something similar in PyMOL? > > Thank you in advance for your help. > > Best Regards, > Anatoliy > > > ________________________________________ > From: Jason Vertrees [jason.vertr...@schrodinger.com] > Sent: Wednesday, April 18, 2012 11:44 AM > To: Anatoliy Volkov > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] visualization of vector data > > Hi Anatoliy, > > I've done this for a few formats including raw data and it's not too > hard. Just figure out the dimensions of your data, grid spacing, etc. > Once you know that, put a CCP4 header on the file and load it as a > CCP4 file. > > An example of this is loading TIFF stacks into CCP4 formatted files. A > script for that can be found here > http://www.pymolwiki.org/index.php/Tiff2ccp4. You can modify the > script for your own format ignoring the TIFF part and focusing on the > CCP4 header part. > > Cheers, > > -- Jason > > On Wed, Apr 18, 2012 at 9:03 AM, Anatoliy Volkov > <anatoliy.vol...@mtsu.edu> wrote: >> Dear PyMOL users, >> >> I know that PyMOL is able to automatically compute and visualize gradient of >> electrostatic potential (ESP). >> However, I have my own codes that can calculate gradient of electron density >> and electric field >> ( - gradient of ESP) from various sources, such as experimental electron >> density models >> and theoretical wavefunctions. >> I am wondering if it is possible to visualize "external" (i.e. precomputed) >> vector data in PyMOL >> (and if yes, how can I do it) ? >> >> Thank you, >> Anatoliy >> --------------------------- >> Anatoliy Volkov, Ph.D. >> Department of Chemistry >> Middle Tennessee State University >> >> >> ------------------------------------------------------------------------------ >> Better than sec? Nothing is better than sec when it comes to >> monitoring Big Data applications. Try Boundary one-second >> resolution app monitoring today. Free. >> http://p.sf.net/sfu/Boundary-dev2dev >> _______________________________________________ >> 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 > PyMOL Product Manager > Schrödinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ 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
