The code threw up a syntax error for me and I don’t know enough python to figure out why, but the CIF approach worked well, thanks very much!
On 22 Sep 2015, at 15:40, Thomas Holder <thomas.hol...@schrodinger.com<mailto:thomas.hol...@schrodinger.com>> wrote: Hi Suzanne & Tsjerk, To get those points in as pseudoatoms, you could also simply place a CIF atom site header above the data and load it as a .cif file. data_foo loop_ _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.ignore_size_a _atom_site.ignore_size_b _atom_site.ignore_size_c 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc The color will be ignored because # is the comment delimiter. The only issue is that all atoms will have the same (empty) identifiers, so in order to select individual atoms, run something like this: PyMOL> alter all, resi=index Cheers, Thomas On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <tsje...@gmail.com<mailto:tsje...@gmail.com>> wrote: Hi Suzanne, I'll make the guess that it's position and color. Are there any lines to be ignored? Probably this will work anyway... Save this in a script called holecgo.py: def holecgo(filename,radius=0.1,name="hole"): data = [ i.split() for i in open(filename) ] data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and k[6].startswith("#") ] cmd.load_cgo([u for x,y,z,r,g,b in data for u in [6.0,r,g,b,7.0,x,y,z,radius]],name) Then in Pymol, do: run holecgo.py holecgo("yourfilename") You can add radius=0.25 or something else to make the spheres larger. Hope it helps, Tsjerk On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <suzanne.sc...@merton.ox.ac.uk<mailto:suzanne.sc...@merton.ox.ac.uk>> wrote: Hi everyone, I hope this isn’t a silly question, but I’m not sure how to do it: I want to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re the output of HOLE implemented in Coot, and have the following format: 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc Where the first three columns are the x, y and z coordinates, the next three are the size of the object, and the last is the colour (which isn’t so important - neither is the size, really). I can’t work out how to import them into PyMOL. If anybody has any ideas, I’d be really grateful! Thanks, Suzanne -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
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