Hi Ben,
The coordinates argument must have a Nx3 shape, that means:
len(coordinates) = number of atoms
len(coordinates[0]) = 3
You can use numpy's reshape() function:
import numpy
coordinates = numpy.asfarray(coordinates).reshape((-1,3))
cmd.load_coords(coordinates, '%prot')
I recommend to prefix the object name with "%" to unambiguously address a named
object or selection. I mention this because I just ran into a common selection
language ambiguity problem myself: I named my object "obj01" and then pasted
your code without changing the object name. The error message was "atom count
mismatch" instead of "invalid selection name". Why? Because "prot" was
evaluated as the selection keyword "protected", so it was a valid (but empty)
selection expression.
Cheers,
Thomas
> On Jan 11, 2018, at 7:43 AM, Benjamin Bailly <bbai...@gmail.com> wrote:
>
> Hi everyone,
>
> I have been scratching my head quite a bit on this one, I am sure there must
> be a simple solution but I can't seem to figure it out.
>
> In short, I would like to record the spacial coordinates of a protein so that
> when I run my script I can fetch it from the PDB and place it exactly where I
> would like it to be.
>
> I used this command to obtain the coordinates, and here is the output I get:
>
> PyMOL>print cmd.get_coords('prot')
> [[159.402 258.709 204.556]
> [159.932 259.514 204.223]
> [158.951 258.206 203.792]
> ...
> [117.662 263.108 309.314]
> [115.591 265.038 307.88 ]
> [116.386 259.713 306.195]]
>
> To load the position in my script I know that I should be able to use the
> following command however I can not figure out the format required:
>
> cmd.load_coords(coordinates, 'prot')
>
> I tried to use all the floats the ones after the other like [1.1, 2.2,
> 3.3,...] and I was close to making it work, but it said the numbers of atoms
> did not match. I read that I should probably used a numpy array but I am not
> sure of its format.
>
> Your help would be much appreciated,
>
> Many thanks
>
> Ben
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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