Re: [PyMOL] Record and load coordinates

[David Hall]

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  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  
>> 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  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.
>> 
> 
> --
> Check out the vibrant tech community on one of the world's most
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Re: [PyMOL] Record and load coordinates

[Benjamin Bailly]

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 
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  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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Re: [PyMOL] Record and load coordinates

[Thomas Holder]

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  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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[PyMOL] Record and load coordinates

[Benjamin Bailly]

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
--
Check out the vibrant tech community on one of the world's most
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