Re: [PyMOL] Ploting coordinates

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 <tho...@sc...<mailto:tho...@sc...>> 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 <ts...@gm...<mailto:ts...@gm...>> 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 <suz...@me...<mailto:suz...@me...>> 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.