The transform matrix you’re using is the identity matrix, so it won’t have any
effect.
-David
> On Jan 11, 2018, at 6:54 PM, Benjamin Bailly <bbai...@gmail.com> wrote:
>
> Hi Thomas,
>
> Thanks for your reply.
>
> So if I am correct, for my protein get_coords fetches a very large matrix of
> thousands and thousands of rows. This could prove very impractical if I want
> to stores those coordinates in a script.
>
> To circumvent this issue I tried the following but it did not seem to work:
>
> print cmd.get_object_matrix('%prot') # to obtain my coordinates in a 4X4
> format
>
> PyMOL>cmd.transform_selection("su", [[1.0,0.0,0.0,0.0], [0.0,1.0,0.0,0.0],
> [0.0,0.0,1.0,0.0], [0.0,0.0,0.0,1.0]], homogenous=1)
> CmdTransformSelection-DEBUG: bad matrix
>
> PyMOL>cmd.transform_selection("su",
> [1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0],
> homogenous=1) # In that case nothing happens
>
> What do you think I am doing wrong?
>
> Many thanks,
>
> Ben
>
> --
>
> Dr Benjamin Bailly | Research Scientist – von Itzstein group
>
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics
> (G26) Room 4.30
>
>
>
> _______________________
>
> Benjamin Bailly
> +61 479 17 66 34 (Australia)
>
>> On 11 January 2018 at 17:26, Thomas Holder <thomas.hol...@schrodinger.com>
>> wrote:
>> 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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