Re: [PyMOL] Write map from list of coordinates.
Hi everyone, I was following this instructions to load a nparray as a map, but I get the error: class Brick has no attribute 'from_numpy' Is it a new feature in chempy, or am I missing something? Cheers, Gian On 2/3/14 3:01 AM, Thomas Holder wrote: Hi Esben, On 02 Feb 2014, at 12:27, Esben Jannik Bjerrum esbenjan...@rocketmail.com wrote: ... I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas? yes, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can import numpy during compilation. Cheers, Thomas -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ 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
Re: [PyMOL] Write map from list of coordinates.
Hi Gian, yes, the from_numpy method is new in PyMOL 1.7. But the underlying import functionality is not new, so you could basically copy the code from that method and create a valid brick instance yourself. Have a look at: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/chempy/brick.py#l28 Cheers, Thomas On 12 Jun 2014, at 16:40, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi everyone, I was following this instructions to load a nparray as a map, but I get the error: class Brick has no attribute 'from_numpy' Is it a new feature in chempy, or am I missing something? Cheers, Gian On 2/3/14 3:01 AM, Thomas Holder wrote: Hi Esben, On 02 Feb 2014, at 12:27, Esben Jannik Bjerrum esbenjan...@rocketmail.com wrote: ... I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas? yes, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can import numpy during compilation. Cheers, Thomas -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ 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
Re: [PyMOL] Write map from list of coordinates.
Hi Jason and Thomas, Thx for you suggestions, Maps are definitely the way to go, and I already have the data it in a numpy array. I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas? Loading directly from Python is the way to go in the future. In the meantime I solved my problem by writing a small script that dumps the data in dx file format, which can subsequently be loaded into PyMOL. #!/usr/bin/python # Esben Jannik Bjerrum 2014 #Write DX format import math nx,ny,nz = 100,100,100 # Number of grid point in X,y,z dim xmin,ymin,zmin = 0,0,0 # coordinate of grid lowest corner. hx = hy = hz = 0.2 #Spacing between grid points f = open(tester.dx,w) f.write(#Comment\n) f.write(object 1 class gridpositions counts %s %s %s\n% (nx,ny,nz)) f.write(origin %s %s %s\n% (xmin,ymin,zmin)) f.write(delta %s 0.0 0.0\ndelta 0.0 %s 0.0\ndelta 0.0 0.0 %s\n%(hx,hy,hz)) f.write(object 2 class gridconnections counts %s %s %s\n%(nx,ny,nz)) f.write(object 3 class array type double rank 0 times %s\n%(nx*ny*nz)) #The data with Z increasing first, then Y, then X. i = 0 for x in range(nx): for y in range(ny): for z in range(nz): #Generation of sample data mx=1.5*(x-nx/2.) my=2*(y-nx/2.) mz=3*(z-nz/2.) #Write values of point number (x,y,z) f.write(%e %(1.-2./math.exp(math.sqrt(mx*mx+my*my+mz*mz)/10.0))) #f.write((%s,%s,%s)%(x,y,z)) if i == 2: f.write(\n) i = 0 else: i += 1 f.write(\n) f.close() Best Regards Esben On Thursday, January 30, 2014 11:45 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: 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=123612991iu=/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
Re: [PyMOL] Write map from list of coordinates.
Hi Esben, On 02 Feb 2014, at 12:27, Esben Jannik Bjerrum esbenjan...@rocketmail.com wrote: ... I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas? yes, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can import numpy during compilation. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/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
Re: [PyMOL] Write map from list of coordinates.
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 -- 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=123612991iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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=123612991iu=/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
Re: [PyMOL] Write map from list of coordinates.
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=123612991iu=/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
