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 ------------------------------------------------------------------------------ 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
