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 <[email protected]> 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
> <[email protected]> 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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