Hi Esben, I just pushed a change to the open-source SVN repo which makes loading maps with a script a little easier. If you have your map in a numpy array, you can do:
yourdata = ... # array with shape (a,b,c) yourgridspacing = (0.2, 0.2, 0.2) # grid spacing from chempy.brick import Brick b = Brick.from_numpy(yourdata, yourgridspacing) cmd.load_brick(b, 'yourmap') Hope that helps. Cheers, Thomas On 30 Jan 2014, at 16:24, Jason Vertrees <jason.vertr...@schrodinger.com> wrote: > Hi Esben, > > I have a list of coordinates on a regular grid with associated floating point > values from a calculation that I want to visualise in PyMOL. Is it nescessary > to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or > can it be loaded directly into a map object via some fancy python code? > > It depends on how you want to visualize the data. If dots/points or other > discrete representations are okay then you can use a XYZ or a modified > structure file. If you want the benefit of a field (volume, gradient, > isosurface) then I suggest the map. > > If you already have the data in a well-formatted brick, check out the asCCP4 > function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That writes the > CCP4 header and data (of a TIFF file, but you can modify that for your > needs). > > If you want, send me a copy of your data. Or, I also have a very poorly > written script that will convert raw volumes of data to CCP4 maps, similar to > the aforementioned script. Email me personally and I can send you a copy if > you prefer (but it's really ugly code). > > Cheers, > > -- Jason > > > On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum > <esbenjan...@rocketmail.com> wrote: > > > > Hi All-knowing Pymol'ers. > > > > I wonder if anyone had a couple of tips/ pointers / script snippets. > > > > I have a list of coordinates on a regular grid with associated floating > > point values from a calculation that I want to visualise in PyMOL. Is it > > nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently > > load it, or can it be loaded directly into a map object via some fancy > > python code? > > > > Best Regards > > Esben Jannik Bjerrum -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ 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
